From 129ec05eb1faaaead16bd7bcb4b76e68b22b114e Mon Sep 17 00:00:00 2001 From: Felix Hennig Date: Thu, 11 Dec 2025 08:09:39 +0000 Subject: [PATCH 01/26] test(website): add a test that validates the wastewater config (#957) --- website/src/types/wastewaterConfig.spec.ts | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 website/src/types/wastewaterConfig.spec.ts 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); + } + }); +}); From 3e7252fdd2f215c3f40cd6db72fcd51815858a72 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 15 Dec 2025 09:19:04 +0100 Subject: [PATCH 02/26] chore(github-actions): bump actions/upload-artifact from 4 to 5 (#890) Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 4 to 5. - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/v4...v5) --- updated-dependencies: - dependency-name: actions/upload-artifact dependency-version: '5' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/e2e.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/e2e.yml b/.github/workflows/e2e.yml index 308b8bcad..1da9ea447 100644 --- a/.github/workflows/e2e.yml +++ b/.github/workflows/e2e.yml @@ -60,7 +60,7 @@ jobs: - name: Run Playwright tests run: npm run e2e - - uses: actions/upload-artifact@v4 + - uses: actions/upload-artifact@v5 if: ${{ !cancelled() }} with: name: playwright-report From 0b751a0856fc11042c0a046e35a931810321381c Mon Sep 17 00:00:00 2001 From: Fabian Engelniederhammer <92720311+fengelniederhammer@users.noreply.github.com> Date: Mon, 15 Dec 2025 10:44:59 +0100 Subject: [PATCH 03/26] chore(ci): consistently use latest version of node (#964) --- .github/workflows/website.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/website.yml b/.github/workflows/website.yml index dd947f1aa..69b3dbcdc 100644 --- a/.github/workflows/website.yml +++ b/.github/workflows/website.yml @@ -37,7 +37,7 @@ jobs: - uses: actions/checkout@v6 - uses: actions/setup-node@v6 with: - node-version: 22 + node-version: lts/* - uses: actions/cache@v4 with: path: ~/.npm From ab3a7c1898fef63f5571951f60ea647d0a16718a Mon Sep 17 00:00:00 2001 From: Felix Hennig Date: Mon, 15 Dec 2025 10:28:13 +0000 Subject: [PATCH 04/26] feat(website): add time frame selector to W-ASAP variant explorer (#961) * feat(website): add time frame selector to W-ASAP variant explorer * feat(website): update text * refactor(website): use const object instead of string literals --- .../pageStateSelectors/wasap/InfoBlocks.tsx | 7 ++ .../VariantExplorerFilter.browser.spec.tsx | 1 + .../wasap/filters/VariantExplorerFilter.tsx | 17 ++++- .../views/wasap/useWasapPageData.ts | 26 ++++++- .../components/views/wasap/wasapPageConfig.ts | 10 +++ website/src/lapis/getMutations.spec.ts | 71 +++++++++++++++++++ website/src/lapis/getMutations.ts | 7 +- website/src/types/wastewaterConfig.ts | 6 +- .../WasapPageStateHandler.ts | 9 +++ 9 files changed, 147 insertions(+), 7 deletions(-) diff --git a/website/src/components/pageStateSelectors/wasap/InfoBlocks.tsx b/website/src/components/pageStateSelectors/wasap/InfoBlocks.tsx index e5bf4cdf4..e8505938d 100644 --- a/website/src/components/pageStateSelectors/wasap/InfoBlocks.tsx +++ b/website/src/components/pageStateSelectors/wasap/InfoBlocks.tsx @@ -97,6 +97,13 @@ export function DefineClinicalSignatureInfo() { indicate that either not all sequences of the variant have the mutation or not all sequences with the mutation belong to the variant (or both).

+ +

Time Frame

+

+ Time frame for sequence selection. Shorter windows reduce dominance of well-sequenced historical + variants, yielding higher Jaccard values for emerging variants with fewer clinical sequences. Use this + filter to exclude variants no longer in circulation when assessing significance of current mutations. +

); } diff --git a/website/src/components/pageStateSelectors/wasap/filters/VariantExplorerFilter.browser.spec.tsx b/website/src/components/pageStateSelectors/wasap/filters/VariantExplorerFilter.browser.spec.tsx index e2e23b58e..dca132918 100644 --- a/website/src/components/pageStateSelectors/wasap/filters/VariantExplorerFilter.browser.spec.tsx +++ b/website/src/components/pageStateSelectors/wasap/filters/VariantExplorerFilter.browser.spec.tsx @@ -17,6 +17,7 @@ describe('VariantExplorerFilter', () => { minProportion: 0.05, minCount: 10, minJaccard: 0.5, + timeFrame: 'all', }; it('calls setPageState when changing sequence type', async ({ routeMockers: { lapis } }) => { diff --git a/website/src/components/pageStateSelectors/wasap/filters/VariantExplorerFilter.tsx b/website/src/components/pageStateSelectors/wasap/filters/VariantExplorerFilter.tsx index 86624a8c3..1186e83d8 100644 --- a/website/src/components/pageStateSelectors/wasap/filters/VariantExplorerFilter.tsx +++ b/website/src/components/pageStateSelectors/wasap/filters/VariantExplorerFilter.tsx @@ -1,6 +1,10 @@ import { Inset } from '../../../../styles/Inset'; import { GsLineageFilter } from '../../../genspectrum/GsLineageFilter'; -import type { WasapVariantFilter } from '../../../views/wasap/wasapPageConfig'; +import { + VARIANT_TIME_FRAME, + type VariantTimeFrame, + type WasapVariantFilter, +} from '../../../views/wasap/wasapPageConfig'; import { SelectorHeadline } from '../../SelectorHeadline'; import { DefineClinicalSignatureInfo } from '../InfoBlocks'; import { LabeledField } from '../utils/LabeledField'; @@ -70,6 +74,17 @@ export function VariantExplorerFilter({ step={0.01} onChange={(v) => setPageState({ ...pageState, minJaccard: v })} /> + + + ); diff --git a/website/src/components/views/wasap/useWasapPageData.ts b/website/src/components/views/wasap/useWasapPageData.ts index ef7f9297a..01082e8a7 100644 --- a/website/src/components/views/wasap/useWasapPageData.ts +++ b/website/src/components/views/wasap/useWasapPageData.ts @@ -1,7 +1,8 @@ -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'; @@ -47,6 +48,7 @@ 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 +99,26 @@ async function fetchMutationSelection( } } +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. diff --git a/website/src/components/views/wasap/wasapPageConfig.ts b/website/src/components/views/wasap/wasapPageConfig.ts index bf5c0af01..9f93e6f21 100644 --- a/website/src/components/views/wasap/wasapPageConfig.ts +++ b/website/src/components/views/wasap/wasapPageConfig.ts @@ -71,6 +71,7 @@ type VariantAnalysisModeConfig = variantAnalysisModeEnabled: true; clinicalLapis: { lapisBaseUrl: string; + dateField: string; lineageField: string; }; filterDefaults: { @@ -157,6 +158,14 @@ 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 type WasapVariantFilter = { mode: 'variant'; sequenceType: SequenceType; @@ -164,6 +173,7 @@ 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/types/wastewaterConfig.ts b/website/src/types/wastewaterConfig.ts index 5fb496f42..3b9ac3c0b 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', @@ -33,6 +33,7 @@ export const wastewaterOrganismConfigs: Record { 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': @@ -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', From 5770669633729978ac5df6250cda3c289165c2be Mon Sep 17 00:00:00 2001 From: Fabian Engelniederhammer <92720311+fengelniederhammer@users.noreply.github.com> Date: Mon, 15 Dec 2025 13:08:52 +0100 Subject: [PATCH 05/26] chore(build): use node 24 in website Docker image (#967) --- Dockerfile_website | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile_website b/Dockerfile_website index 02b5f0977..823df38e9 100644 --- a/Dockerfile_website +++ b/Dockerfile_website @@ -1,6 +1,6 @@ # Dockerfile for the website # This is here so that the build context can access the backend config files -FROM node:22-alpine AS base +FROM node:24-alpine AS base WORKDIR /app COPY website/package.json website/package-lock.json website/patches ./ From a6ea5b9cbc63d4635889fe014d8df0e6fa4e3668 Mon Sep 17 00:00:00 2001 From: Fabian Engelniederhammer <92720311+fengelniederhammer@users.noreply.github.com> Date: Mon, 15 Dec 2025 13:29:52 +0100 Subject: [PATCH 06/26] refactor(website): migrate compare variants data display to React (#963) * refactor(website): migrate compare variants data display to React resolves #960 * chore(website): update memo * chore(website): delete now unused component * chore(website): bump components --- website/package-lock.json | 163 +++++------------- website/package.json | 2 +- .../genspectrum/GsMutationComparison.astro | 25 --- .../genspectrum/GsMutationComparison.tsx | 35 ++++ .../GenericCompareVariantsDataDisplay.tsx | 72 ++++++++ .../GenericCompareVariantsPage.astro | 55 ++---- .../compareVariants/SelectVariants.astro | 14 -- .../views/compareVariants/SelectVariants.tsx | 18 ++ 8 files changed, 179 insertions(+), 205 deletions(-) delete mode 100644 website/src/components/genspectrum/GsMutationComparison.astro create mode 100644 website/src/components/genspectrum/GsMutationComparison.tsx create mode 100644 website/src/components/views/compareVariants/GenericCompareVariantsDataDisplay.tsx delete mode 100644 website/src/components/views/compareVariants/SelectVariants.astro create mode 100644 website/src/components/views/compareVariants/SelectVariants.tsx diff --git a/website/package-lock.json b/website/package-lock.json index c4becf25d..14af7a826 100644 --- a/website/package-lock.json +++ b/website/package-lock.json @@ -11,7 +11,7 @@ "dependencies": { "@astrojs/node": "^9.4.4", "@auth/core": "^0.37.4", - "@genspectrum/dashboard-components": "^1.11.1", + "@genspectrum/dashboard-components": "^1.12.0", "@tanstack/react-query": "^5.90.1", "astro": "^5.13.10", "auth-astro": "^4.2.0", @@ -110,7 +110,6 @@ "dev": true, "license": "MIT", "optional": true, - "peer": true, "dependencies": { "@csstools/css-calc": "^2.1.2", "@csstools/css-color-parser": "^3.0.8", @@ -125,8 +124,7 @@ "integrity": "sha512-JNAzZcXrCt42VGLuYz0zfAzDfAvJWW6AfYlDBQyDV5DClI2m5sAmK+OIO7s59XfsRsWHp02jAJrRadPRGTt6SQ==", "dev": true, "license": "ISC", - "optional": true, - "peer": true + "optional": true }, "node_modules/@astrojs/check": { "version": "0.9.4", @@ -151,7 +149,8 @@ "version": "2.12.2", "resolved": "https://registry.npmjs.org/@astrojs/compiler/-/compiler-2.12.2.tgz", "integrity": "sha512-w2zfvhjNCkNMmMMOn5b0J8+OmUaBL1o40ipMvqcG6NRpdC+lKxmTi48DT8Xw0SzJ3AfmeFLB45zXZXtmbsjcgw==", - "license": "MIT" + "license": "MIT", + "peer": true }, "node_modules/@astrojs/internal-helpers": { "version": "0.7.3", @@ -310,6 +309,7 @@ "resolved": "https://registry.npmjs.org/@auth/core/-/core-0.37.4.tgz", "integrity": "sha512-HOXJwXWXQRhbBDHlMU0K/6FT1v+wjtzdKhsNg0ZN7/gne6XPsIrjZ4daMcFnbq0Z/vsAbYBinQhhua0d77v7qw==", "license": "ISC", + "peer": true, "dependencies": { "@panva/hkdf": "^1.2.1", "jose": "^5.9.6", @@ -365,6 +365,7 @@ "integrity": "sha512-2BCOP7TN8M+gVDj7/ht3hsaO/B/n5oDbiAyyvnRlNOs+u1o+JWNYTQrmpuNp1/Wq2gcFrI01JAW+paEKDMx/CA==", "dev": true, "license": "MIT", + "peer": true, "dependencies": { "@babel/code-frame": "^7.27.1", "@babel/generator": "^7.28.3", @@ -711,7 +712,6 @@ ], "license": "MIT-0", "optional": true, - "peer": true, "engines": { "node": ">=18" } @@ -733,7 +733,6 @@ ], "license": "MIT", "optional": true, - "peer": true, "engines": { "node": ">=18" }, @@ -759,7 +758,6 @@ ], "license": "MIT", "optional": true, - "peer": true, "dependencies": { "@csstools/color-helpers": "^5.0.2", "@csstools/css-calc": "^2.1.2" @@ -772,53 +770,6 @@ "@csstools/css-tokenizer": "^3.0.3" } }, - "node_modules/@csstools/css-parser-algorithms": { - "version": "3.0.4", - "resolved": "https://registry.npmjs.org/@csstools/css-parser-algorithms/-/css-parser-algorithms-3.0.4.tgz", - "integrity": "sha512-Up7rBoV77rv29d3uKHUIVubz1BTcgyUK72IvCQAbfbMv584xHcGKCKbWh7i8hPrRJ7qU4Y8IO3IY9m+iTB7P3A==", - "dev": true, - "funding": [ - { - "type": "github", - "url": "https://github.com/sponsors/csstools" - }, - { - "type": "opencollective", - "url": "https://opencollective.com/csstools" - } - ], - "license": "MIT", - "optional": true, - "peer": true, - "engines": { - "node": ">=18" - }, - "peerDependencies": { - "@csstools/css-tokenizer": "^3.0.3" - } - }, - "node_modules/@csstools/css-tokenizer": { - "version": "3.0.3", - "resolved": "https://registry.npmjs.org/@csstools/css-tokenizer/-/css-tokenizer-3.0.3.tgz", - "integrity": "sha512-UJnjoFsmxfKUdNYdWgOB0mWUypuLvAfQPH1+pyvRJs6euowbFkFC6P13w1l8mJyi3vxYMxc9kld5jZEGRQs6bw==", - "dev": true, - "funding": [ - { - "type": "github", - "url": "https://github.com/sponsors/csstools" - }, - { - "type": "opencollective", - "url": "https://opencollective.com/csstools" - } - ], - "license": "MIT", - "optional": true, - "peer": true, - "engines": { - "node": ">=18" - } - }, "node_modules/@dabh/diagnostics": { "version": "2.0.3", "resolved": "https://registry.npmjs.org/@dabh/diagnostics/-/diagnostics-2.0.3.tgz", @@ -1513,9 +1464,9 @@ "license": "MIT" }, "node_modules/@genspectrum/dashboard-components": { - "version": "1.11.1", - "resolved": "https://registry.npmjs.org/@genspectrum/dashboard-components/-/dashboard-components-1.11.1.tgz", - "integrity": "sha512-nsyGuETthi5kAwb4shb21vPtobSq96bPfSvxLPTAFbNDH9wNsjC0X7otnKvQqKWxYNE3H4j561LZJinwqlRiiA==", + "version": "1.12.0", + "resolved": "https://registry.npmjs.org/@genspectrum/dashboard-components/-/dashboard-components-1.12.0.tgz", + "integrity": "sha512-RW7j1Q1TqtP7dKR//BaIrvCfaQmVZ/Z5ZTWDUDs5o+uhliSQKlnCk44qALmxa3MsgFVcBK8st5s+S3kKqS+ZaQ==", "license": "AGPL-3.0-only", "dependencies": { "@floating-ui/dom": "^1.6.5", @@ -3209,6 +3160,7 @@ "integrity": "sha512-o4PXJQidqJl82ckFaXUeoAW+XysPLauYI43Abki5hABd853iMhitooc6znOnczgbTYmEP6U6/y1ZyKAIsvMKGg==", "dev": true, "license": "MIT", + "peer": true, "dependencies": { "@babel/code-frame": "^7.10.4", "@babel/runtime": "^7.12.5", @@ -3468,6 +3420,7 @@ "integrity": "sha512-t4yC+vtgnkYjNSKlFx1jkAhH8LgTo2N/7Qvi83kdEaUtMDiwpbLAktKDaAMlRcJ5eSxZkH74eEGt1ky31d7kfQ==", "dev": true, "license": "MIT", + "peer": true, "dependencies": { "@types/prop-types": "*", "csstype": "^3.0.2" @@ -3479,6 +3432,7 @@ "integrity": "sha512-P4t6saawp+b/dFrUr2cvkVsfvPguwsxtH6dNIYRllMsefqFzkZk5UIjzyDOv5g1dXIPdG4Sp1yCR4Z6RCUsG/Q==", "dev": true, "license": "MIT", + "peer": true, 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{ "whatwg-encoding": "^3.1.1" }, @@ -7799,7 +7728,6 @@ "dev": true, "license": "MIT", "optional": true, - "peer": true, "dependencies": { "agent-base": "^7.1.0", "debug": "^4.3.4" @@ -7815,7 +7743,6 @@ "dev": true, "license": "MIT", "optional": true, - "peer": true, "dependencies": { "agent-base": "^7.1.2", "debug": "4" @@ -7831,7 +7758,6 @@ "dev": true, "license": "MIT", "optional": true, - "peer": true, "dependencies": { "safer-buffer": ">= 2.1.2 < 3.0.0" }, @@ -8255,8 +8181,7 @@ "integrity": "sha512-bCYeRA2rVibKZd+s2625gGnGF/t7DSqDs4dP7CrLA1m7jKWz6pps0LpYLJN8Q64HtmPKJ1hrN3nzPNKFEKOUiQ==", "dev": true, "license": "MIT", - "optional": true, - "peer": true + "optional": true }, "node_modules/is-regex": { "version": "1.2.1", @@ -8504,7 +8429,6 @@ "dev": true, "license": "MIT", "optional": true, - "peer": true, "dependencies": { "cssstyle": "^4.2.1", "data-urls": "^5.0.0", @@ -8546,7 +8470,6 @@ "dev": true, "license": "BSD-3-Clause", "optional": true, - "peer": true, "dependencies": { "tldts": "^6.1.32" }, @@ -8561,7 +8484,6 @@ "dev": true, "license": "MIT", "optional": true, - "peer": true, "engines": { "node": ">=18" } @@ -10174,6 +10096,7 @@ "dev": true, "hasInstallScript": true, "license": "MIT", + "peer": true, "dependencies": { "@bundled-es-modules/cookie": "^2.0.1", "@bundled-es-modules/statuses": "^1.0.1", @@ -10353,8 +10276,7 @@ "integrity": "sha512-/ieB+mDe4MrrKMT8z+mQL8klXydZWGR5Dowt4RAGKbJ3kIGEx3X4ljUo+6V73IXtUPWgfOlU5B9MlGxFO5T+cA==", "dev": true, "license": "MIT", - "optional": true, - "peer": true + "optional": true }, "node_modules/oauth4webapi": { "version": "3.3.0", @@ -11043,6 +10965,7 @@ "resolved": "https://registry.npmjs.org/preact/-/preact-10.24.3.tgz", "integrity": "sha512-Z2dPnBnMUfyQfSQ+GBdsGa16hz35YmLmtTLhM169uW944hYL6xzTYkJjC07j+Wosz733pMWx0fgON3JNw1jJQA==", "license": "MIT", + "peer": true, "funding": { "type": "opencollective", "url": "https://opencollective.com/preact" @@ -11072,6 +10995,7 @@ "resolved": 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"sha512-wS+hAgJShR0KhEvPJArfuPVN1+Hz1t0Y6n5jLrGQbkb4urgPE/0Rve+1kMB1v/oWgHgm4WIcV+i7F2pTVj+2iQ==", "license": "MIT", + "peer": true, "dependencies": { "loose-envify": "^1.1.0" }, @@ -11363,6 +11290,7 @@ "resolved": "https://registry.npmjs.org/react-dom/-/react-dom-18.3.1.tgz", "integrity": "sha512-5m4nQKp+rZRb09LNH59GM4BxTh9251/ylbKIbpe7TpGxfJ+9kv6BLkLBXIjjspbgbnIBNqlI23tRnTWT0snUIw==", "license": "MIT", + "peer": true, "dependencies": { "loose-envify": "^1.1.0", "scheduler": "^0.23.2" @@ -11831,6 +11759,7 @@ "resolved": "https://registry.npmjs.org/rollup/-/rollup-4.34.9.tgz", "integrity": "sha512-nF5XYqWWp9hx/LrpC8sZvvvmq0TeTjQgaZHYmAgwysT9nh8sWnZhBnM8ZyVbbJFIQBLwHDNoMqsBZBbUo4U8sQ==", "license": "MIT", + "peer": true, "dependencies": { "@types/estree": "1.0.6" }, @@ -11870,8 +11799,7 @@ "integrity": "sha512-guoltQEx+9aMf2gDZ0s62EcV8lsXR+0w8915TC3ITdn2YueuNjdAYh/levpU9nFaoChh9RUS5ZdQMrKfVEN9tw==", "dev": true, "license": "MIT", - "optional": true, - "peer": true + "optional": true }, "node_modules/run-parallel": { "version": "1.2.0", @@ -11994,8 +11922,7 @@ "integrity": "sha512-YZo3K82SD7Riyi0E1EQPojLz7kpepnSQI9IyPbHHg1XXXevb5dJI7tpyN2ADxGcQbHG7vcyRHk0cbwqcQriUtg==", "dev": true, "license": "MIT", - "optional": true, - "peer": true + "optional": true }, "node_modules/sass-formatter": { "version": "0.7.9", @@ -12014,7 +11941,6 @@ "dev": true, "license": "ISC", "optional": true, - "peer": true, "dependencies": { "xmlchars": "^2.2.0" }, @@ -12713,8 +12639,7 @@ "integrity": "sha512-9QNk5KwDF+Bvz+PyObkmSYjI5ksVUYtjW7AU22r2NKcfLJcXp96hkDWU3+XndOsUb+AQ9QhfzfCT2O+CNWT5Tw==", "dev": true, "license": "MIT", - "optional": true, - "peer": true + "optional": true }, "node_modules/synckit": { "version": "0.9.2", @@ -12738,7 +12663,8 @@ "resolved": "https://registry.npmjs.org/tailwindcss/-/tailwindcss-4.1.13.tgz", "integrity": "sha512-i+zidfmTqtwquj4hMEwdjshYYgMbOrPzb9a0M3ZgNa0JMoZeFC6bxZvO8yr8ozS6ix2SDz0+mvryPeBs2TFE+w==", "dev": true, - "license": "MIT" + "license": "MIT", + "peer": true }, "node_modules/tapable": { "version": "2.2.3", @@ -12860,7 +12786,6 @@ "dev": true, "license": "MIT", "optional": true, - "peer": true, "dependencies": { "tldts-core": "^6.1.86" }, @@ -12874,8 +12799,7 @@ "integrity": "sha512-Je6p7pkk+KMzMv2XXKmAE3McmolOQFdxkKw0R8EYNr7sELW46JqnNeTX8ybPiQgvg1ymCoF8LXs5fzFaZvJPTA==", "dev": true, "license": "MIT", - "optional": true, - "peer": true + "optional": true }, "node_modules/tmp": { "version": "0.0.33", @@ -12974,7 +12898,6 @@ "dev": true, "license": "MIT", "optional": true, - "peer": true, "dependencies": { "punycode": "^2.3.1" }, @@ -13191,6 +13114,7 @@ "resolved": "https://registry.npmjs.org/typescript/-/typescript-5.9.2.tgz", "integrity": "sha512-CWBzXQrc/qOkhidw1OzBTQuYRbfyxDXJMVJ1XNwUHGROVmuaeiEm3OslpZ1RV96d7SKKjZKrSJu3+t/xlw3R9A==", "license": "Apache-2.0", + "peer": true, "bin": { "tsc": "bin/tsc", "tsserver": "bin/tsserver" @@ -13575,6 +13499,7 @@ "resolved": "https://registry.npmjs.org/vite/-/vite-6.3.6.tgz", "integrity": "sha512-0msEVHJEScQbhkbVTb/4iHZdJ6SXp/AvxL2sjwYQFfBqleHtnCqv1J3sa9zbWz/6kW1m9Tfzn92vW+kZ1WV6QA==", "license": "MIT", + "peer": true, "dependencies": { "esbuild": "^0.25.0", "fdir": "^6.4.4", @@ -13706,6 +13631,7 @@ "integrity": "sha512-LUCP5ev3GURDysTWiP47wRRUpLKMOfPh+yKTx3kVIEiu5KOMeqzpnYNsKyOoVrULivR8tLcks4+lga33Whn90A==", "dev": true, "license": "MIT", + "peer": true, "dependencies": { "@types/chai": "^5.2.2", "@vitest/expect": "3.2.4", @@ -14064,7 +13990,6 @@ "dev": true, "license": "MIT", "optional": true, - "peer": true, "dependencies": { "xml-name-validator": "^5.0.0" }, @@ -14089,7 +14014,6 @@ "dev": true, "license": "BSD-2-Clause", "optional": true, - "peer": true, "engines": { "node": ">=12" } @@ -14101,7 +14025,6 @@ "dev": true, "license": "MIT", "optional": true, - "peer": true, "dependencies": { "iconv-lite": "0.6.3" }, @@ -14116,7 +14039,6 @@ "dev": true, "license": "MIT", "optional": true, - "peer": true, "engines": { "node": ">=12" } @@ -14128,7 +14050,6 @@ "dev": true, "license": "MIT", "optional": true, - "peer": true, "dependencies": { "tr46": "^5.1.0", "webidl-conversions": "^7.0.0" @@ -14287,6 +14208,7 @@ "resolved": "https://registry.npmjs.org/winston/-/winston-3.17.0.tgz", "integrity": "sha512-DLiFIXYC5fMPxaRg832S6F5mJYvePtmO5G9v9IgUFPhXm9/GkXarH/TUrBAVzhTCzAj9anE/+GjrgXp/54nOgw==", "license": "MIT", + "peer": true, "dependencies": { "@colors/colors": "^1.6.0", "@dabh/diagnostics": "^2.0.2", @@ -14410,7 +14332,6 @@ "dev": true, "license": "Apache-2.0", "optional": true, - "peer": true, "engines": { "node": ">=18" } @@ -14421,8 +14342,7 @@ "integrity": "sha512-JZnDKK8B0RCDw84FNdDAIpZK+JuJw+s7Lz8nksI7SIuU3UXJJslUthsi+uWBUYOwPFwW7W7PRLRfUKpxjtjFCw==", "dev": true, "license": "MIT", - "optional": true, - "peer": true + "optional": true }, "node_modules/xxhash-wasm": { "version": "1.1.0", @@ -14703,6 +14623,7 @@ "resolved": "https://registry.npmjs.org/zod/-/zod-3.25.76.tgz", "integrity": "sha512-gzUt/qt81nXsFGKIFcC3YnfEAx5NkunCfnDlvuBSSFS02bcXu4Lmea0AFIUwbLWxWPx3d9p8S5QoaujKcNQxcQ==", "license": "MIT", + "peer": true, "funding": { "url": "https://github.com/sponsors/colinhacks" } diff --git a/website/package.json b/website/package.json index e67541fa6..c5a791dc5 100644 --- a/website/package.json +++ b/website/package.json @@ -25,7 +25,7 @@ "dependencies": { "@astrojs/node": "^9.4.4", "@auth/core": "^0.37.4", - "@genspectrum/dashboard-components": "^1.11.1", + "@genspectrum/dashboard-components": "^1.12.0", "@tanstack/react-query": "^5.90.1", "astro": "^5.13.10", "auth-astro": "^4.2.0", diff --git a/website/src/components/genspectrum/GsMutationComparison.astro b/website/src/components/genspectrum/GsMutationComparison.astro deleted file mode 100644 index edb4f07df..000000000 --- a/website/src/components/genspectrum/GsMutationComparison.astro +++ /dev/null @@ -1,25 +0,0 @@ ---- -import type { NamedLapisFilter, SequenceType } from '@genspectrum/dashboard-components/util'; - -import { defaultTablePageSize } from '../../views/View'; -import ComponentWrapper from '../ComponentWrapper.astro'; - -interface Props { - lapisFilters: NamedLapisFilter[]; - sequenceType: SequenceType; - height?: string; - pageSize?: number; -} - -const { lapisFilters, sequenceType, height, pageSize } = Astro.props; ---- - - - - diff --git a/website/src/components/genspectrum/GsMutationComparison.tsx b/website/src/components/genspectrum/GsMutationComparison.tsx new file mode 100644 index 000000000..eac5b1a70 --- /dev/null +++ b/website/src/components/genspectrum/GsMutationComparison.tsx @@ -0,0 +1,35 @@ +import type { NamedLapisFilter, SequenceType } from '@genspectrum/dashboard-components/util'; +import type { FC } from 'react'; + +import { defaultTablePageSize } from '../../views/View'; +import { ComponentWrapper } from '../ComponentWrapper.tsx'; + +export type GsMutationComparisonProps = { + lapisFilters: NamedLapisFilter[]; + sequenceType: SequenceType; + height?: string; + pageSize?: number; +}; + +export const GsMutationComparison: FC = ({ + lapisFilters, + sequenceType, + height, + pageSize, +}) => { + return ( + + + + ); +}; diff --git a/website/src/components/views/compareVariants/GenericCompareVariantsDataDisplay.tsx b/website/src/components/views/compareVariants/GenericCompareVariantsDataDisplay.tsx new file mode 100644 index 000000000..2b57434cd --- /dev/null +++ b/website/src/components/views/compareVariants/GenericCompareVariantsDataDisplay.tsx @@ -0,0 +1,72 @@ +import { type FC, useMemo } from 'react'; + +import { SelectVariants } from './SelectVariants.tsx'; +import type { OrganismsConfig } from '../../../config.ts'; +import { chooseGranularityBasedOnDateRange } from '../../../util/chooseGranularityBasedOnDateRange.ts'; +import type { CompareVariantsData } from '../../../views/View.ts'; +import { type OrganismWithViewKey, Routing } from '../../../views/routing.ts'; +import { compareVariantsViewKey } from '../../../views/viewKeys.ts'; +import { ComponentsGrid } from '../../ComponentsGrid.tsx'; +import { GsMutationComparison } from '../../genspectrum/GsMutationComparison.tsx'; +import { GsPrevalenceOverTime } from '../../genspectrum/GsPrevalenceOverTime.tsx'; + +export type GenericCompareVariantsDataDisplayProps = { + organismViewKey: `${OrganismWithViewKey}.${typeof compareVariantsViewKey}`; + organismsConfig: OrganismsConfig; + pageState: CompareVariantsData; +}; + +const componentHeight = '540px'; // prevalence over time table with 10 rows + +export const GenericCompareVariantsDataDisplay: FC = ({ + organismViewKey, + organismsConfig, + pageState, +}) => { + const view = useMemo( + () => new Routing(organismsConfig).getOrganismView(organismViewKey), + [organismsConfig, organismViewKey], + ); + + const datasetLapisFilter = view.pageStateHandler.datasetFilterToLapisFilter(pageState.datasetFilter); + const timeGranularity = chooseGranularityBasedOnDateRange({ + earliestDate: new Date(view.organismConstants.earliestDate), + dateRange: pageState.datasetFilter.dateFilters[view.organismConstants.mainDateField], + }); + + const numeratorLapisFilters = view.pageStateHandler.variantFiltersToNamedLapisFilters(pageState); + + const notEnoughVariantsSelected = pageState.variants.size < 2; + + return ( +
+ {notEnoughVariantsSelected ? ( + + ) : ( + + + + + + )} +
+ ); +}; diff --git a/website/src/components/views/compareVariants/GenericCompareVariantsPage.astro b/website/src/components/views/compareVariants/GenericCompareVariantsPage.astro index 8d077ac5d..76727768d 100644 --- a/website/src/components/views/compareVariants/GenericCompareVariantsPage.astro +++ b/website/src/components/views/compareVariants/GenericCompareVariantsPage.astro @@ -1,14 +1,10 @@ --- -import SelectVariants from './SelectVariants.astro'; +import { GenericCompareVariantsDataDisplay } from './GenericCompareVariantsDataDisplay'; import { isStaging, getDashboardsConfig } from '../../../config'; import SingleVariantOrganismPageLayout from '../../../layouts/OrganismPage/SingleVariantOrganismPageLayout.astro'; -import { chooseGranularityBasedOnDateRange } from '../../../util/chooseGranularityBasedOnDateRange'; import { type OrganismViewKey, type OrganismWithViewKey } from '../../../views/routing'; import { ServerSide } from '../../../views/serverSideRouting'; import { compareVariantsViewKey } from '../../../views/viewKeys'; -import ComponentsGrid from '../../ComponentsGrid.astro'; -import GsMutationComparison from '../../genspectrum/GsMutationComparison.astro'; -import GsPrevalenceOverTime from '../../genspectrum/GsPrevalenceOverTime.astro'; import { CompareVariantsPageStateSelector } from '../../pageStateSelectors/CompareVariantsPageStateSelector'; import { CompareVariantsSelectorFallback } from '../../pageStateSelectors/FallbackElement'; import { sanitizeForFilename } from '../compareSideBySide/toDownloadLink'; @@ -24,16 +20,8 @@ const view = ServerSide.routing.getOrganismView(organismViewKey); const pageState = view.pageStateHandler.parsePageStateFromUrl(Astro.url); -const datasetLapisFilter = view.pageStateHandler.datasetFilterToLapisFilter(pageState.datasetFilter); -const timeGranularity = chooseGranularityBasedOnDateRange({ - earliestDate: new Date(view.organismConstants.earliestDate), - dateRange: pageState.datasetFilter.dateFilters[view.organismConstants.mainDateField], -}); - const numeratorLapisFilters = view.pageStateHandler.variantFiltersToNamedLapisFilters(pageState); - const notEnoughVariantsSelected = pageState.variants.size < 2; - const downloadLinks = notEnoughVariantsSelected ? [] : numeratorLapisFilters.map(({ lapisFilter, displayName }) => ({ @@ -42,47 +30,26 @@ const downloadLinks = notEnoughVariantsSelected downloadFileBasename: `${organism}_${sanitizeForFilename(displayName)}_accessions`, })); -const componentHeight = '540px'; // prevalence over time table with 10 rows +const organismConfig = getDashboardsConfig().dashboards.organisms; --- - { - notEnoughVariantsSelected ? ( - - ) : ( - - - - - - ) - } +
+ +
diff --git a/website/src/components/views/compareVariants/SelectVariants.astro b/website/src/components/views/compareVariants/SelectVariants.astro deleted file mode 100644 index cc249d57a..000000000 --- a/website/src/components/views/compareVariants/SelectVariants.astro +++ /dev/null @@ -1,14 +0,0 @@ ---- -import { PageHeadline } from '../../../styles/containers/PageHeadline'; ---- - -
- Compare Variants -
-

To proceed, please select two or more variants in the variant filter.

-

- Note that the dataset filter is applied to all variants. Adjust the dataset filter as needed to refine your - selection. -

-
-
diff --git a/website/src/components/views/compareVariants/SelectVariants.tsx b/website/src/components/views/compareVariants/SelectVariants.tsx new file mode 100644 index 000000000..b0aabb861 --- /dev/null +++ b/website/src/components/views/compareVariants/SelectVariants.tsx @@ -0,0 +1,18 @@ +import type { FC } from 'react'; + +import { PageHeadline } from '../../../styles/containers/PageHeadline.tsx'; + +export const SelectVariants: FC = () => { + return ( +
+ Compare Variants +
+

To proceed, please select two or more variants in the variant filter.

+

+ Note that the dataset filter is applied to all variants. Adjust the dataset filter as needed to + refine your selection. +

+
+
+ ); +}; From 4392c0cfda5e6906d31b8f87882cc2ff8d2c95f5 Mon Sep 17 00:00:00 2001 From: Felix Hennig Date: Mon, 15 Dec 2025 12:42:40 +0000 Subject: [PATCH 07/26] test(website): add WasapPageStateHandler unit test (#962) * test(website): add WasapPageStateHandler unit test * test(website): add timeframe to test after rebase --- .../components/views/wasap/wasapPageConfig.ts | 4 +- .../WasapPageStateHandler.spec.ts | 322 ++++++++++++++++++ .../WasapPageStateHandler.ts | 6 +- 3 files changed, 327 insertions(+), 5 deletions(-) create mode 100644 website/src/views/pageStateHandlers/WasapPageStateHandler.spec.ts diff --git a/website/src/components/views/wasap/wasapPageConfig.ts b/website/src/components/views/wasap/wasapPageConfig.ts index 9f93e6f21..52c98df41 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'; @@ -144,7 +144,7 @@ export type WasapAnalysisMode = 'manual' | 'variant' | 'resistance' | 'untracked export type WasapBaseFilter = { locationName?: string; samplingDate?: DateRangeOption; - granularity: string; + granularity: TemporalGranularity; excludeEmpty: boolean; }; diff --git a/website/src/views/pageStateHandlers/WasapPageStateHandler.spec.ts b/website/src/views/pageStateHandlers/WasapPageStateHandler.spec.ts new file mode 100644 index 000000000..fd6a5da5c --- /dev/null +++ b/website/src/views/pageStateHandlers/WasapPageStateHandler.spec.ts @@ -0,0 +1,322 @@ +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)', + 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 0d9a85e61..d16b8e31f 100644 --- a/website/src/views/pageStateHandlers/WasapPageStateHandler.ts +++ b/website/src/views/pageStateHandlers/WasapPageStateHandler.ts @@ -1,9 +1,9 @@ -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, @@ -96,7 +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', }; From ad5eec6c41bbdd521e7391c890618f61a0fe9df1 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 16 Dec 2025 09:21:16 +0100 Subject: [PATCH 08/26] chore(github-actions): bump actions/upload-artifact from 5 to 6 (#970) Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 5 to 6. - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/v5...v6) --- updated-dependencies: - dependency-name: actions/upload-artifact dependency-version: '6' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/e2e.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/e2e.yml b/.github/workflows/e2e.yml index 1da9ea447..898ff2fc4 100644 --- a/.github/workflows/e2e.yml +++ b/.github/workflows/e2e.yml @@ -60,7 +60,7 @@ jobs: - name: Run Playwright tests run: npm run e2e - - uses: actions/upload-artifact@v5 + - uses: actions/upload-artifact@v6 if: ${{ !cancelled() }} with: name: playwright-report From 94b8aeb85bc3cf48a613aa58c5f82fe815e0c25b Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 16 Dec 2025 09:21:43 +0100 Subject: [PATCH 09/26] chore(github-actions): bump actions/cache from 4 to 5 (#971) Bumps [actions/cache](https://github.com/actions/cache) from 4 to 5. - [Release notes](https://github.com/actions/cache/releases) - [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md) - [Commits](https://github.com/actions/cache/compare/v4...v5) --- updated-dependencies: - dependency-name: actions/cache dependency-version: '5' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/commitlint.yml | 2 +- .github/workflows/e2e.yml | 2 +- .github/workflows/website.yml | 4 ++-- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/commitlint.yml b/.github/workflows/commitlint.yml index 15d84dfbb..54d7437f9 100644 --- a/.github/workflows/commitlint.yml +++ b/.github/workflows/commitlint.yml @@ -21,7 +21,7 @@ jobs: with: node-version: lts/* - - uses: actions/cache@v4 + - uses: actions/cache@v5 with: path: ~/.npm key: ${{ runner.os }}-node-${{ hashFiles('package-lock.json') }} diff --git a/.github/workflows/e2e.yml b/.github/workflows/e2e.yml index 898ff2fc4..fc416fcdd 100644 --- a/.github/workflows/e2e.yml +++ b/.github/workflows/e2e.yml @@ -13,7 +13,7 @@ jobs: with: node-version: lts/* - name: Cache .npm - uses: actions/cache@v4 + uses: actions/cache@v5 with: path: ~/.npm key: ${{ runner.os }}-node-${{ hashFiles('lapis-e2e/**/package-lock.json') }} diff --git a/.github/workflows/website.yml b/.github/workflows/website.yml index 69b3dbcdc..6ba0d4a9b 100644 --- a/.github/workflows/website.yml +++ b/.github/workflows/website.yml @@ -17,7 +17,7 @@ jobs: - uses: actions/setup-node@v6 with: node-version: lts/* - - uses: actions/cache@v4 + - uses: actions/cache@v5 with: path: ~/.npm key: ${{ runner.os }}-node-${{ hashFiles('package-lock.json') }} @@ -38,7 +38,7 @@ jobs: - uses: actions/setup-node@v6 with: node-version: lts/* - - uses: actions/cache@v4 + - uses: actions/cache@v5 with: path: ~/.npm key: ${{ runner.os }}-node-${{ hashFiles('package-lock.json') }} From 169819a676b5fa010ccf84cf6e5b5d65d8a9d08a Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 15 Dec 2025 19:17:56 +0000 Subject: [PATCH 10/26] chore(website): bump the minorandpatch group across 1 directory with 31 updates Bumps the minorandpatch group with 28 updates in the /website directory: | Package | From | To | | --- | --- | --- | | [@astrojs/node](https://github.com/withastro/astro/tree/HEAD/packages/integrations/node) | `9.4.4` | `9.5.1` | | [@tanstack/react-query](https://github.com/TanStack/query/tree/HEAD/packages/react-query) | `5.90.1` | `5.90.12` | | [axios](https://github.com/axios/axios) | `1.12.2` | `1.13.2` | | [cookie](https://github.com/jshttp/cookie) | `1.0.2` | `1.1.1` | | [dayjs](https://github.com/iamkun/dayjs) | `1.11.18` | `1.11.19` | | [katex](https://github.com/KaTeX/KaTeX) | `0.16.25` | `0.16.27` | | [patch-package](https://github.com/ds300/patch-package) | `8.0.0` | `8.0.1` | | [winston](https://github.com/winstonjs/winston) | `3.17.0` | `3.19.0` | | [yaml](https://github.com/eemeli/yaml) | `2.8.1` | `2.8.2` | | [@astrojs/check](https://github.com/withastro/astro/tree/HEAD/packages/language-tools/astro-check) | `0.9.4` | `0.9.6` | | [@astrojs/react](https://github.com/withastro/astro/tree/HEAD/packages/integrations/react) | `4.3.1` | `4.4.2` | | [@eslint/js](https://github.com/eslint/eslint/tree/HEAD/packages/js) | `9.36.0` | `9.39.2` | | [@iconify/tailwind4](https://github.com/iconify/iconify-tailwind/tree/HEAD/packages/plugin) | `1.0.6` | `1.2.0` | | [@playwright/test](https://github.com/microsoft/playwright) | `1.55.0` | `1.57.0` | | [@tailwindcss/vite](https://github.com/tailwindlabs/tailwindcss/tree/HEAD/packages/@tailwindcss-vite) | `4.1.13` | `4.1.18` | | [@tanstack/eslint-plugin-query](https://github.com/TanStack/query/tree/HEAD/packages/eslint-plugin-query) | `5.90.1` | `5.91.2` | | [@testing-library/jest-dom](https://github.com/testing-library/jest-dom) | `6.8.0` | `6.9.1` | | [@testing-library/react](https://github.com/testing-library/react-testing-library) | `16.3.0` | `16.3.1` | | [@typescript-eslint/eslint-plugin](https://github.com/typescript-eslint/typescript-eslint/tree/HEAD/packages/eslint-plugin) | `8.44.1` | `8.50.0` | | [@typescript-eslint/parser](https://github.com/typescript-eslint/typescript-eslint/tree/HEAD/packages/parser) | `8.44.1` | `8.50.0` | | [daisyui](https://github.com/saadeghi/daisyui/tree/HEAD/packages/daisyui) | `5.1.14` | `5.5.14` | | [eslint](https://github.com/eslint/eslint) | `9.36.0` | `9.39.2` | | [eslint-plugin-astro](https://github.com/ota-meshi/eslint-plugin-astro) | `1.3.1` | `1.5.0` | | [msw](https://github.com/mswjs/msw) | `2.11.3` | `2.12.4` | | [prettier](https://github.com/prettier/prettier) | `3.6.2` | `3.7.4` | | [prettier-plugin-tailwindcss](https://github.com/tailwindlabs/prettier-plugin-tailwindcss) | `0.6.14` | `0.7.2` | | [typescript](https://github.com/microsoft/TypeScript) | `5.9.2` | `5.9.3` | | [typescript-eslint](https://github.com/typescript-eslint/typescript-eslint/tree/HEAD/packages/typescript-eslint) | `8.44.1` | `8.50.0` | Updates `@astrojs/node` from 9.4.4 to 9.5.1 - [Release notes](https://github.com/withastro/astro/releases) - [Changelog](https://github.com/withastro/astro/blob/main/packages/integrations/node/CHANGELOG.md) - [Commits](https://github.com/withastro/astro/commits/@astrojs/node@9.5.1/packages/integrations/node) Updates `@tanstack/react-query` from 5.90.1 to 5.90.12 - [Release notes](https://github.com/TanStack/query/releases) - [Changelog](https://github.com/TanStack/query/blob/main/packages/react-query/CHANGELOG.md) - [Commits](https://github.com/TanStack/query/commits/@tanstack/react-query@5.90.12/packages/react-query) Updates `astro` from 5.13.10 to 5.16.5 - [Release notes](https://github.com/withastro/astro/releases) - [Changelog](https://github.com/withastro/astro/blob/main/packages/astro/CHANGELOG.md) - [Commits](https://github.com/withastro/astro/commits/astro@5.16.5/packages/astro) Updates `axios` from 1.12.2 to 1.13.2 - [Release notes](https://github.com/axios/axios/releases) - [Changelog](https://github.com/axios/axios/blob/v1.x/CHANGELOG.md) - [Commits](https://github.com/axios/axios/compare/v1.12.2...v1.13.2) Updates `cookie` from 1.0.2 to 1.1.1 - [Release notes](https://github.com/jshttp/cookie/releases) - [Commits](https://github.com/jshttp/cookie/compare/v1.0.2...v1.1.1) Updates `dayjs` from 1.11.18 to 1.11.19 - [Release notes](https://github.com/iamkun/dayjs/releases) - [Changelog](https://github.com/iamkun/dayjs/blob/dev/CHANGELOG.md) - [Commits](https://github.com/iamkun/dayjs/compare/v1.11.18...v1.11.19) Updates `katex` from 0.16.25 to 0.16.27 - [Release notes](https://github.com/KaTeX/KaTeX/releases) - [Changelog](https://github.com/KaTeX/KaTeX/blob/main/CHANGELOG.md) - [Commits](https://github.com/KaTeX/KaTeX/compare/v0.16.25...v0.16.27) Updates `patch-package` from 8.0.0 to 8.0.1 - [Release notes](https://github.com/ds300/patch-package/releases) - [Changelog](https://github.com/ds300/patch-package/blob/master/CHANGELOG.md) - [Commits](https://github.com/ds300/patch-package/commits) Updates `winston` from 3.17.0 to 3.19.0 - [Release notes](https://github.com/winstonjs/winston/releases) - [Changelog](https://github.com/winstonjs/winston/blob/master/CHANGELOG.md) - [Commits](https://github.com/winstonjs/winston/compare/v3.17.0...v3.19.0) Updates `yaml` from 2.8.1 to 2.8.2 - [Release notes](https://github.com/eemeli/yaml/releases) - [Commits](https://github.com/eemeli/yaml/compare/v2.8.1...v2.8.2) Updates `@astrojs/check` from 0.9.4 to 0.9.6 - [Release notes](https://github.com/withastro/astro/releases) - [Changelog](https://github.com/withastro/astro/blob/main/packages/language-tools/astro-check/CHANGELOG.md) - [Commits](https://github.com/withastro/astro/commits/@astrojs/check@0.9.6/packages/language-tools/astro-check) Updates `@astrojs/react` from 4.3.1 to 4.4.2 - [Release notes](https://github.com/withastro/astro/releases) - [Changelog](https://github.com/withastro/astro/blob/main/packages/integrations/react/CHANGELOG.md) - [Commits](https://github.com/withastro/astro/commits/@astrojs/react@4.4.2/packages/integrations/react) Updates `@eslint/js` from 9.36.0 to 9.39.2 - [Release notes](https://github.com/eslint/eslint/releases) - [Commits](https://github.com/eslint/eslint/commits/v9.39.2/packages/js) Updates `@iconify/tailwind4` from 1.0.6 to 1.2.0 - [Commits](https://github.com/iconify/iconify-tailwind/commits/HEAD/packages/plugin) Updates `@playwright/test` from 1.55.0 to 1.57.0 - [Release notes](https://github.com/microsoft/playwright/releases) - [Commits](https://github.com/microsoft/playwright/compare/v1.55.0...v1.57.0) Updates `@tailwindcss/vite` from 4.1.13 to 4.1.18 - [Release notes](https://github.com/tailwindlabs/tailwindcss/releases) - [Changelog](https://github.com/tailwindlabs/tailwindcss/blob/main/CHANGELOG.md) - [Commits](https://github.com/tailwindlabs/tailwindcss/commits/v4.1.18/packages/@tailwindcss-vite) Updates `@tanstack/eslint-plugin-query` from 5.90.1 to 5.91.2 - [Release notes](https://github.com/TanStack/query/releases) - [Changelog](https://github.com/TanStack/query/blob/main/packages/eslint-plugin-query/CHANGELOG.md) - [Commits](https://github.com/TanStack/query/commits/@tanstack/eslint-plugin-query@5.91.2/packages/eslint-plugin-query) Updates `@testing-library/jest-dom` from 6.8.0 to 6.9.1 - [Release notes](https://github.com/testing-library/jest-dom/releases) - [Changelog](https://github.com/testing-library/jest-dom/blob/main/CHANGELOG.md) - [Commits](https://github.com/testing-library/jest-dom/compare/v6.8.0...v6.9.1) Updates `@testing-library/react` from 16.3.0 to 16.3.1 - [Release notes](https://github.com/testing-library/react-testing-library/releases) - [Changelog](https://github.com/testing-library/react-testing-library/blob/main/CHANGELOG.md) - [Commits](https://github.com/testing-library/react-testing-library/compare/v16.3.0...v16.3.1) Updates `@typescript-eslint/eslint-plugin` from 8.44.1 to 8.50.0 - [Release notes](https://github.com/typescript-eslint/typescript-eslint/releases) - [Changelog](https://github.com/typescript-eslint/typescript-eslint/blob/main/packages/eslint-plugin/CHANGELOG.md) - [Commits](https://github.com/typescript-eslint/typescript-eslint/commits/v8.50.0/packages/eslint-plugin) Updates `@typescript-eslint/parser` from 8.44.1 to 8.50.0 - [Release notes](https://github.com/typescript-eslint/typescript-eslint/releases) - [Changelog](https://github.com/typescript-eslint/typescript-eslint/blob/main/packages/parser/CHANGELOG.md) - [Commits](https://github.com/typescript-eslint/typescript-eslint/commits/v8.50.0/packages/parser) Updates `daisyui` from 5.1.14 to 5.5.14 - [Release notes](https://github.com/saadeghi/daisyui/releases) - [Changelog](https://github.com/saadeghi/daisyui/blob/master/CHANGELOG.md) - [Commits](https://github.com/saadeghi/daisyui/commits/v5.5.14/packages/daisyui) Updates `eslint` from 9.36.0 to 9.39.2 - [Release notes](https://github.com/eslint/eslint/releases) - [Commits](https://github.com/eslint/eslint/compare/v9.36.0...v9.39.2) Updates `eslint-plugin-astro` from 1.3.1 to 1.5.0 - [Release notes](https://github.com/ota-meshi/eslint-plugin-astro/releases) - [Changelog](https://github.com/ota-meshi/eslint-plugin-astro/blob/main/CHANGELOG.md) - [Commits](https://github.com/ota-meshi/eslint-plugin-astro/compare/v1.3.1...v1.5.0) Updates `msw` from 2.11.3 to 2.12.4 - [Release notes](https://github.com/mswjs/msw/releases) - [Changelog](https://github.com/mswjs/msw/blob/main/CHANGELOG.md) - [Commits](https://github.com/mswjs/msw/compare/v2.11.3...v2.12.4) Updates `playwright` from 1.55.0 to 1.57.0 - [Release notes](https://github.com/microsoft/playwright/releases) - [Commits](https://github.com/microsoft/playwright/compare/v1.55.0...v1.57.0) Updates `prettier` from 3.6.2 to 3.7.4 - [Release notes](https://github.com/prettier/prettier/releases) - [Changelog](https://github.com/prettier/prettier/blob/main/CHANGELOG.md) - [Commits](https://github.com/prettier/prettier/compare/3.6.2...3.7.4) Updates `prettier-plugin-tailwindcss` from 0.6.14 to 0.7.2 - [Release notes](https://github.com/tailwindlabs/prettier-plugin-tailwindcss/releases) - [Changelog](https://github.com/tailwindlabs/prettier-plugin-tailwindcss/blob/main/CHANGELOG.md) - [Commits](https://github.com/tailwindlabs/prettier-plugin-tailwindcss/compare/v0.6.14...v0.7.2) Updates `tailwindcss` from 4.1.13 to 4.1.18 - [Release notes](https://github.com/tailwindlabs/tailwindcss/releases) - [Changelog](https://github.com/tailwindlabs/tailwindcss/blob/main/CHANGELOG.md) - [Commits](https://github.com/tailwindlabs/tailwindcss/commits/v4.1.18/packages/tailwindcss) Updates `typescript` from 5.9.2 to 5.9.3 - [Release notes](https://github.com/microsoft/TypeScript/releases) - [Commits](https://github.com/microsoft/TypeScript/compare/v5.9.2...v5.9.3) Updates `typescript-eslint` from 8.44.1 to 8.50.0 - [Release notes](https://github.com/typescript-eslint/typescript-eslint/releases) - [Changelog](https://github.com/typescript-eslint/typescript-eslint/blob/main/packages/typescript-eslint/CHANGELOG.md) - [Commits](https://github.com/typescript-eslint/typescript-eslint/commits/v8.50.0/packages/typescript-eslint) --- updated-dependencies: - dependency-name: "@astrojs/node" dependency-version: 9.5.1 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: minorandpatch - dependency-name: "@tanstack/react-query" dependency-version: 5.90.12 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: minorandpatch - dependency-name: astro dependency-version: 5.16.5 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: minorandpatch - dependency-name: axios dependency-version: 1.13.2 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: minorandpatch - dependency-name: cookie dependency-version: 1.1.1 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: minorandpatch - dependency-name: dayjs dependency-version: 1.11.19 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: minorandpatch - dependency-name: katex dependency-version: 0.16.27 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: minorandpatch - dependency-name: patch-package dependency-version: 8.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: minorandpatch - dependency-name: winston dependency-version: 3.19.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: minorandpatch - dependency-name: yaml dependency-version: 2.8.2 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: minorandpatch - dependency-name: "@astrojs/check" dependency-version: 0.9.6 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: minorandpatch - dependency-name: "@astrojs/react" dependency-version: 4.4.2 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: minorandpatch - dependency-name: "@eslint/js" dependency-version: 9.39.2 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: minorandpatch - dependency-name: "@iconify/tailwind4" dependency-version: 1.2.0 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: minorandpatch - dependency-name: "@playwright/test" dependency-version: 1.57.0 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: minorandpatch - dependency-name: "@tailwindcss/vite" dependency-version: 4.1.18 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: minorandpatch - dependency-name: "@tanstack/eslint-plugin-query" dependency-version: 5.91.2 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: minorandpatch - dependency-name: "@testing-library/jest-dom" dependency-version: 6.9.1 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: minorandpatch - dependency-name: "@testing-library/react" dependency-version: 16.3.1 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: minorandpatch - dependency-name: "@typescript-eslint/eslint-plugin" dependency-version: 8.50.0 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: minorandpatch - dependency-name: "@typescript-eslint/parser" dependency-version: 8.50.0 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: minorandpatch - dependency-name: daisyui dependency-version: 5.5.14 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: minorandpatch - dependency-name: eslint dependency-version: 9.39.2 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: minorandpatch - dependency-name: eslint-plugin-astro dependency-version: 1.5.0 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: minorandpatch - dependency-name: msw dependency-version: 2.12.4 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: minorandpatch - dependency-name: playwright dependency-version: 1.57.0 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: minorandpatch - dependency-name: prettier dependency-version: 3.7.4 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: minorandpatch - dependency-name: prettier-plugin-tailwindcss dependency-version: 0.7.2 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: minorandpatch - dependency-name: tailwindcss dependency-version: 4.1.18 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: minorandpatch - dependency-name: typescript dependency-version: 5.9.3 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: minorandpatch - dependency-name: typescript-eslint dependency-version: 8.50.0 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: minorandpatch ... Signed-off-by: dependabot[bot] --- website/package-lock.json | 2294 +++++++++++++++++-------------------- website/package.json | 56 +- 2 files changed, 1108 insertions(+), 1242 deletions(-) diff --git a/website/package-lock.json b/website/package-lock.json index 14af7a826..54a935833 100644 --- a/website/package-lock.json +++ b/website/package-lock.json @@ -9,64 +9,64 @@ "version": "0.0.1", "hasInstallScript": true, "dependencies": { - "@astrojs/node": "^9.4.4", + "@astrojs/node": "^9.5.1", "@auth/core": "^0.37.4", "@genspectrum/dashboard-components": "^1.12.0", - "@tanstack/react-query": "^5.90.1", + "@tanstack/react-query": "^5.90.12", "astro": "^5.13.10", "auth-astro": "^4.2.0", - "axios": "^1.12.2", - "cookie": "^1.0.2", - "dayjs": "^1.11.18", - "katex": "^0.16.25", - "patch-package": "^8.0.0", + "axios": "^1.13.2", + "cookie": "^1.1.1", + "dayjs": "^1.11.19", + "katex": "^0.16.27", + "patch-package": "^8.0.1", "react": "^18.3.1", "react-dom": "^18.3.1", "react-katex": "^3.1.0", "react-toastify": "^11.0.5", "uuid": "^11.1.0", - "winston": "^3.17.0", + "winston": "^3.19.0", "winston-daily-rotate-file": "^5.0.0", - "yaml": "^2.8.1" + "yaml": "^2.8.2" }, "devDependencies": { - "@astrojs/check": "^0.9.4", - "@astrojs/react": "^4.3.1", - "@eslint/js": "^9.36.0", + "@astrojs/check": "^0.9.6", + "@astrojs/react": "^4.4.2", + "@eslint/js": "^9.39.2", "@iconify-json/mdi": "^1.2.3", "@iconify-json/mdi-light": "^1.2.2", - "@iconify/tailwind4": "^1.0.6", - "@playwright/test": "^1.55.0", - "@tailwindcss/vite": "^4.1.13", - "@tanstack/eslint-plugin-query": "^5.90.1", + "@iconify/tailwind4": "^1.2.0", + "@playwright/test": "^1.57.0", + "@tailwindcss/vite": "^4.1.18", + "@tanstack/eslint-plugin-query": "^5.91.2", "@testing-library/dom": "^10.4.1", - "@testing-library/jest-dom": "^6.8.0", - "@testing-library/react": "^16.3.0", + "@testing-library/jest-dom": "^6.9.1", + "@testing-library/react": "^16.3.1", "@testing-library/user-event": "^14.6.1", "@types/node": "^24.5.2", "@types/react": "^18.3.12", "@types/react-dom": "^18.3.1", "@types/react-katex": "^3.0.4", "@types/topojson-specification": "^1.0.5", - 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"dev": true, - "license": "MIT", - "engines": { - "node": ">=8.0.0 || >=10.0.0" - } - }, - "node_modules/yaml-language-server/node_modules/vscode-languageserver": { - "version": "7.0.0", - "resolved": "https://registry.npmjs.org/vscode-languageserver/-/vscode-languageserver-7.0.0.tgz", - "integrity": "sha512-60HTx5ID+fLRcgdHfmz0LDZAXYEV68fzwG0JWwEPBode9NuMYTIxuYXPg4ngO8i8+Ou0lM7y6GzaYWbiDL0drw==", - "dev": true, - "license": "MIT", - "dependencies": { - "vscode-languageserver-protocol": "3.16.0" - }, - "bin": { - "installServerIntoExtension": "bin/installServerIntoExtension" - } - }, - "node_modules/yaml-language-server/node_modules/vscode-languageserver-protocol": { - "version": "3.16.0", - "resolved": "https://registry.npmjs.org/vscode-languageserver-protocol/-/vscode-languageserver-protocol-3.16.0.tgz", - "integrity": "sha512-sdeUoAawceQdgIfTI+sdcwkiK2KU+2cbEYA0agzM2uqaUy2UpnnGHtWTHVEtS0ES4zHU0eMFRGN+oQgDxlD66A==", - "dev": true, - "license": "MIT", - "dependencies": { - "vscode-jsonrpc": "6.0.0", - "vscode-languageserver-types": "3.16.0" - } - }, - "node_modules/yaml-language-server/node_modules/vscode-languageserver-types": { - "version": "3.16.0", - "resolved": "https://registry.npmjs.org/vscode-languageserver-types/-/vscode-languageserver-types-3.16.0.tgz", - "integrity": "sha512-k8luDIWJWyenLc5ToFQQMaSrqCHiLwyKPHKPQZ5zz21vM+vIVUSvsRpcbiECH4WR88K2XZqc4ScRcZ7nk/jbeA==", - "dev": true, - "license": "MIT" - }, "node_modules/yaml-language-server/node_modules/yaml": { - "version": "2.2.2", - "resolved": "https://registry.npmjs.org/yaml/-/yaml-2.2.2.tgz", - "integrity": "sha512-CBKFWExMn46Foo4cldiChEzn7S7SRV+wqiluAb6xmueD/fGyRHIhX8m14vVGgeFWjN540nKCNVj6P21eQjgTuA==", + "version": "2.7.1", + "resolved": "https://registry.npmjs.org/yaml/-/yaml-2.7.1.tgz", + "integrity": "sha512-10ULxpnOCQXxJvBgxsn9ptjq6uviG/htZKk9veJGhlqn3w/DxQ631zFF+nlQXLwmImeS5amR2dl2U8sg6U9jsQ==", "dev": true, "license": "ISC", + "bin": { + "yaml": "bin.mjs" + }, "engines": { "node": ">= 14" } @@ -14629,12 +14495,12 @@ } }, "node_modules/zod-to-json-schema": { - 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"axios": "^1.12.2", - "cookie": "^1.0.2", - "dayjs": "^1.11.18", - "katex": "^0.16.25", - "patch-package": "^8.0.0", + "axios": "^1.13.2", + "cookie": "^1.1.1", + "dayjs": "^1.11.19", + "katex": "^0.16.27", + "patch-package": "^8.0.1", "react": "^18.3.1", "react-dom": "^18.3.1", "react-katex": "^3.1.0", "react-toastify": "^11.0.5", "uuid": "^11.1.0", - "winston": "^3.17.0", + "winston": "^3.19.0", "winston-daily-rotate-file": "^5.0.0", - "yaml": "^2.8.1" + "yaml": "^2.8.2" }, "devDependencies": { - "@astrojs/check": "^0.9.4", - "@astrojs/react": "^4.3.1", - "@eslint/js": "^9.36.0", + "@astrojs/check": "^0.9.6", + "@astrojs/react": "^4.4.2", + "@eslint/js": "^9.39.2", "@iconify-json/mdi": "^1.2.3", "@iconify-json/mdi-light": "^1.2.2", - "@iconify/tailwind4": "^1.0.6", - "@playwright/test": "^1.55.0", - "@tailwindcss/vite": "^4.1.13", - "@tanstack/eslint-plugin-query": "^5.90.1", + "@iconify/tailwind4": "^1.2.0", + "@playwright/test": "^1.57.0", + "@tailwindcss/vite": "^4.1.18", + "@tanstack/eslint-plugin-query": "^5.91.2", "@testing-library/dom": "^10.4.1", - "@testing-library/jest-dom": "^6.8.0", - "@testing-library/react": "^16.3.0", + "@testing-library/jest-dom": "^6.9.1", + "@testing-library/react": "^16.3.1", "@testing-library/user-event": "^14.6.1", "@types/node": "^24.5.2", "@types/react": "^18.3.12", "@types/react-dom": "^18.3.1", "@types/react-katex": "^3.0.4", "@types/topojson-specification": "^1.0.5", - "@typescript-eslint/eslint-plugin": "^8.44.1", - "@typescript-eslint/parser": "^8.44.1", + "@typescript-eslint/eslint-plugin": "^8.50.0", + "@typescript-eslint/parser": "^8.50.0", "@vitest/browser": "^3.2.4", "astro-eslint-parser": "^1.2.2", - "daisyui": "^5.1.14", + "daisyui": "^5.5.14", "dotenv": "^16.5.0", - "eslint": "^9.36.0", - "eslint-plugin-astro": "^1.3.1", + "eslint": "^9.39.2", + "eslint-plugin-astro": "^1.5.0", "eslint-plugin-import": "^2.32.0", "eslint-plugin-react": "^7.37.5", "eslint-plugin-react-hooks": "^5.2.0", - "msw": "^2.11.3", + "msw": "^2.12.4", "playwright": "^1.55.0", - "prettier": "^3.6.2", + "prettier": "^3.7.4", "prettier-plugin-astro": "^0.14.1", - "prettier-plugin-tailwindcss": "^0.6.14", + "prettier-plugin-tailwindcss": "^0.7.2", "tailwindcss": "^4.0.9", - "typescript": "^5.9.2", - "typescript-eslint": "^8.44.1", + "typescript": "^5.9.3", + "typescript-eslint": "^8.50.0", "vitest": "^3.2.4", "vitest-browser-react": "^1.0.1", "zod": "^3.25.74" From cd368ae2c2196edec8e8a83fe0c77aae9d4b1e90 Mon Sep 17 00:00:00 2001 From: Fabian Engelniederhammer Date: Tue, 16 Dec 2025 09:25:09 +0100 Subject: [PATCH 11/26] chore(website): format --- website/src/pages/index.astro | 4 ++-- website/src/views/BaseView.ts | 3 +-- .../pageStateHandlers/SequencingEffortsPageStateHandler.ts | 6 +++--- .../pageStateHandlers/SingleVariantPageStateHandler.ts | 6 +++--- 4 files changed, 9 insertions(+), 10 deletions(-) diff --git a/website/src/pages/index.astro b/website/src/pages/index.astro index 6887477bc..f7c21db3e 100644 --- a/website/src/pages/index.astro +++ b/website/src/pages/index.astro @@ -110,8 +110,8 @@ import { Page } from '../types/pages'; Feedback, suggestions, bug reports and active contributions are highly welcome, please create an issue in our Github repository - . For general questions, please contact Chaoran Chen (chaoran.chen@bsse.ethz.ch). For media requests, please - reach out to ETH Zurich Media Relations (mediarelations@hk.ethz.ch). A list of all team members can be found + . For general questions, please contact Chaoran Chen (chaoran.chen@bsse.ethz.ch). For media requests, please reach + out to ETH Zurich Media Relations (mediarelations@hk.ethz.ch). A list of all team members can be found here . diff --git a/website/src/views/BaseView.ts b/website/src/views/BaseView.ts index 11381f4e4..492d416fd 100644 --- a/website/src/views/BaseView.ts +++ b/website/src/views/BaseView.ts @@ -19,8 +19,7 @@ export abstract class BaseView< PageState extends object, Constants extends OrganismConstants, StateHandler extends PageStateHandler, -> 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( From 90aa99ebe15195a24bfa8cb342cb5c1346f12156 Mon Sep 17 00:00:00 2001 From: Fabian Engelniederhammer Date: Tue, 16 Dec 2025 09:44:51 +0100 Subject: [PATCH 12/26] chore(website): fix lints --- website/src/components/genspectrum/GsMutationFilter.tsx | 2 +- website/src/components/pageStateSelectors/DynamicDateFilter.tsx | 2 +- website/src/components/views/wasap/WasapPage.tsx | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/website/src/components/genspectrum/GsMutationFilter.tsx b/website/src/components/genspectrum/GsMutationFilter.tsx index a8d97e663..ea4a63f96 100644 --- a/website/src/components/genspectrum/GsMutationFilter.tsx +++ b/website/src/components/genspectrum/GsMutationFilter.tsx @@ -13,7 +13,7 @@ export function GsMutationFilter({ initialValue, width, enabledMutationTypes, - onMutationChange = () => {}, + onMutationChange, }: { width?: string; initialValue?: MutationFilter | string[] | undefined; diff --git a/website/src/components/pageStateSelectors/DynamicDateFilter.tsx b/website/src/components/pageStateSelectors/DynamicDateFilter.tsx index 26a966a73..61c447345 100644 --- a/website/src/components/pageStateSelectors/DynamicDateFilter.tsx +++ b/website/src/components/pageStateSelectors/DynamicDateFilter.tsx @@ -46,7 +46,7 @@ export function DynamicDateFilter({ // When the value has a "Custom" label, try to match it back to one of the generated options // by comparing dateFrom and dateTo. If there's a match, use that option's label instead of "Custom". const normalizedValue = useMemo(() => { - if (value === undefined || value.label !== CustomDateRangeLabel) { + if (value?.label !== CustomDateRangeLabel) { return value; } diff --git a/website/src/components/views/wasap/WasapPage.tsx b/website/src/components/views/wasap/WasapPage.tsx index 0f87beea0..52f94c8c7 100644 --- a/website/src/components/views/wasap/WasapPage.tsx +++ b/website/src/components/views/wasap/WasapPage.tsx @@ -79,7 +79,7 @@ export const WasapPageInner: FC = ({ wastewaterOrganism, current ) : (
- {displayMutations !== undefined && displayMutations.length === 0 ? ( + {displayMutations?.length === 0 ? ( ) : ( Date: Tue, 16 Dec 2025 11:34:24 +0100 Subject: [PATCH 13/26] refactor(website): migrate "compare to baseline" page to React (#966) * refactor(website): migrate "compare to baseline" page to React resolves #965 * chore(website): fix * chore(website): better memo --- .../GenericCompareToBaselineDataDisplay.tsx | 53 +++++++++++++++++++ .../GenericCompareToBaselinePage.astro | 41 +++++--------- .../compareToBaseline/SelectBaseline.astro | 15 ------ .../compareToBaseline/SelectBaseline.tsx | 19 +++++++ website/tests/CompareToBaselinePage.ts | 38 +++++++++++++ website/tests/compareToBaseline.spec.ts | 27 ++++++++++ website/tests/compareVariants.spec.ts | 23 +------- website/tests/e2e.fixture.ts | 5 ++ website/tests/helpers.ts | 22 +++++++- 9 files changed, 176 insertions(+), 67 deletions(-) create mode 100644 website/src/components/views/compareToBaseline/GenericCompareToBaselineDataDisplay.tsx delete mode 100644 website/src/components/views/compareToBaseline/SelectBaseline.astro create mode 100644 website/src/components/views/compareToBaseline/SelectBaseline.tsx create mode 100644 website/tests/CompareToBaselinePage.ts create mode 100644 website/tests/compareToBaseline.spec.ts diff --git a/website/src/components/views/compareToBaseline/GenericCompareToBaselineDataDisplay.tsx b/website/src/components/views/compareToBaseline/GenericCompareToBaselineDataDisplay.tsx new file mode 100644 index 000000000..39dc1bb01 --- /dev/null +++ b/website/src/components/views/compareToBaseline/GenericCompareToBaselineDataDisplay.tsx @@ -0,0 +1,53 @@ +import { type FC, useMemo } from 'react'; + +import { SelectBaseline } from './SelectBaseline.tsx'; +import type { OrganismsConfig } from '../../../config.ts'; +import { chooseGranularityBasedOnDateRange } from '../../../util/chooseGranularityBasedOnDateRange.ts'; +import { ComponentHeight } from '../../../views/OrganismConstants.ts'; +import type { CompareToBaselineData } from '../../../views/View.ts'; +import { type OrganismWithViewKey, Routing } from '../../../views/routing.ts'; +import { compareToBaselineViewKey } from '../../../views/viewKeys.ts'; +import { ComponentsGrid } from '../../ComponentsGrid.tsx'; +import { GsPrevalenceOverTime } from '../../genspectrum/GsPrevalenceOverTime.tsx'; + +export type GenericCompareToBaselineDisplayProps = { + organismViewKey: `${OrganismWithViewKey}.${typeof compareToBaselineViewKey}`; + organismsConfig: OrganismsConfig; + pageState: CompareToBaselineData; +}; + +export const GenericCompareToBaselineDataDisplay: FC = ({ + organismViewKey, + organismsConfig, + pageState, +}) => { + const view = useMemo( + () => new Routing(organismsConfig).getOrganismView(organismViewKey), + [organismsConfig, organismViewKey], + ); + + const baselineLapisFilter = view.pageStateHandler.baselineFilterToLapisFilter(pageState); + const timeGranularity = chooseGranularityBasedOnDateRange({ + earliestDate: new Date(view.organismConstants.earliestDate), + dateRange: pageState.datasetFilter.dateFilters[view.organismConstants.mainDateField], + }); + + const numeratorLapisFilters = view.pageStateHandler.variantFiltersToNamedLapisFilters(pageState); + const noVariantSelected = pageState.variants.size < 1; + + return noVariantSelected ? ( + + ) : ( + + + + ); +}; diff --git a/website/src/components/views/compareToBaseline/GenericCompareToBaselinePage.astro b/website/src/components/views/compareToBaseline/GenericCompareToBaselinePage.astro index 9229c10c3..5095db10d 100644 --- a/website/src/components/views/compareToBaseline/GenericCompareToBaselinePage.astro +++ b/website/src/components/views/compareToBaseline/GenericCompareToBaselinePage.astro @@ -1,14 +1,10 @@ --- -import SelectBaseline from './SelectBaseline.astro'; +import { GenericCompareToBaselineDataDisplay } from './GenericCompareToBaselineDataDisplay'; import { isStaging, getDashboardsConfig } from '../../../config'; import SingleVariantOrganismPageLayout from '../../../layouts/OrganismPage/SingleVariantOrganismPageLayout.astro'; -import { chooseGranularityBasedOnDateRange } from '../../../util/chooseGranularityBasedOnDateRange'; -import { ComponentHeight } from '../../../views/OrganismConstants'; import { type OrganismViewKey, type OrganismWithViewKey } from '../../../views/routing'; import { ServerSide } from '../../../views/serverSideRouting'; import { compareToBaselineViewKey } from '../../../views/viewKeys'; -import ComponentsGrid from '../../ComponentsGrid.astro'; -import GsPrevalenceOverTime from '../../genspectrum/GsPrevalenceOverTime.astro'; import { CompareVariantsToBaselineStateSelector } from '../../pageStateSelectors/CompareVariantsToBaselineStateSelector'; import { CompareToBaselineSelectorFallback } from '../../pageStateSelectors/FallbackElement'; import { sanitizeForFilename } from '../compareSideBySide/toDownloadLink'; @@ -24,12 +20,6 @@ const view = ServerSide.routing.getOrganismView(organismViewKey); const pageState = view.pageStateHandler.parsePageStateFromUrl(Astro.url); -const baselineLapisFilter = view.pageStateHandler.baselineFilterToLapisFilter(pageState); -const timeGranularity = chooseGranularityBasedOnDateRange({ - earliestDate: new Date(view.organismConstants.earliestDate), - dateRange: pageState.datasetFilter.dateFilters[view.organismConstants.mainDateField], -}); - const numeratorLapisFilters = view.pageStateHandler.variantFiltersToNamedLapisFilters(pageState); const noVariantSelected = pageState.variants.size < 1; @@ -40,6 +30,8 @@ const downloadLinks = noVariantSelected filter: lapisFilter, downloadFileBasename: `${organism}_${sanitizeForFilename(displayName)}_accessions`, })); + +const organismConfig = getDashboardsConfig().dashboards.organisms; --- @@ -47,27 +39,18 @@ const downloadLinks = noVariantSelected slot='filters' initialPageState={pageState} organismViewKey={organismViewKey} - organismsConfig={getDashboardsConfig().dashboards.organisms} + organismsConfig={organismConfig} enableAdvancedQueryFilter={isStaging()} client:only='react' > - { - noVariantSelected ? ( - - ) : ( - - - - ) - } +
+ +
diff --git a/website/src/components/views/compareToBaseline/SelectBaseline.astro b/website/src/components/views/compareToBaseline/SelectBaseline.astro deleted file mode 100644 index c01f303b1..000000000 --- a/website/src/components/views/compareToBaseline/SelectBaseline.astro +++ /dev/null @@ -1,15 +0,0 @@ ---- -import { PageHeadline } from '../../../styles/containers/PageHeadline'; ---- - -
- Analyze a variant compared to a baseline -
-

To proceed, please select a variant filter.

-

- If no baseline is selected all sequences will be used as a baseline for comparing against sequences with a - specified variant. Note that the dataset filter is applied to the entire dataset including both the baseline - and variant subsets. Adjust the dataset filter as needed to refine your selection. -

-
-
diff --git a/website/src/components/views/compareToBaseline/SelectBaseline.tsx b/website/src/components/views/compareToBaseline/SelectBaseline.tsx new file mode 100644 index 000000000..c2132159c --- /dev/null +++ b/website/src/components/views/compareToBaseline/SelectBaseline.tsx @@ -0,0 +1,19 @@ +import type { FC } from 'react'; + +import { PageHeadline } from '../../../styles/containers/PageHeadline.tsx'; + +export const SelectBaseline: FC = () => { + return ( +
+ Analyze a variant compared to a baseline +
+

To proceed, please select a variant filter.

+

+ If no baseline is selected all sequences will be used as a baseline for comparing against sequences + with a specified variant. Note that the dataset filter is applied to the entire dataset including + both the baseline and variant subsets. Adjust the dataset filter as needed to refine your selection. +

+
+
+ ); +}; diff --git a/website/tests/CompareToBaselinePage.ts b/website/tests/CompareToBaselinePage.ts new file mode 100644 index 000000000..9f41d2784 --- /dev/null +++ b/website/tests/CompareToBaselinePage.ts @@ -0,0 +1,38 @@ +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 lineageFieldLocator.first().fill(lineage); + + const selectedLineage = this.page.getByRole('option', { name: lineage, exact: false }); + await selectedLineage.first().click(); + } + + if (options.mutation) { + await this.mutationField.first().fill(options.mutation); + await this.mutationField.first().press('Enter'); + } + } +} 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..6a655f331 100644 --- a/website/tests/e2e.fixture.ts +++ b/website/tests/e2e.fixture.ts @@ -1,11 +1,13 @@ import { test as base } from '@playwright/test'; +import { CompareToBaselinePage } from './CompareToBaselinePage.ts'; import { CompareVariantsPage } from './CompareVariantsPage.ts'; import { SequencingEffortsPage } from './SequencingEffortsPage.ts'; type E2EFixture = { compareVariantsPage: CompareVariantsPage; sequencingEffortsPage: SequencingEffortsPage; + compareToBaselinePage: CompareToBaselinePage; }; export const test = base.extend({ @@ -15,4 +17,7 @@ export const test = base.extend({ sequencingEffortsPage: async ({ page }, use) => { await use(new SequencingEffortsPage(page)); }, + compareToBaselinePage: async ({ page }, use) => { + await use(new CompareToBaselinePage(page)); + }, }); diff --git a/website/tests/helpers.ts b/website/tests/helpers.ts index 55120cbc5..2e3edba44 100644 --- a/website/tests/helpers.ts +++ b/website/tests/helpers.ts @@ -1,7 +1,27 @@ -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.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' }, +}; From ae2e48eb4fc6d19e7094a95fbecff474b9118069 Mon Sep 17 00:00:00 2001 From: Fabian Engelniederhammer <92720311+fengelniederhammer@users.noreply.github.com> Date: Wed, 17 Dec 2025 09:59:36 +0100 Subject: [PATCH 14/26] ci(website): only execute e2e tests against Chromium on feature branches (#976) to speed up tests --- .github/workflows/e2e.yml | 7 ++++++- website/package.json | 3 ++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/.github/workflows/e2e.yml b/.github/workflows/e2e.yml index fc416fcdd..5f6f2e4c0 100644 --- a/.github/workflows/e2e.yml +++ b/.github/workflows/e2e.yml @@ -57,9 +57,14 @@ jobs: WEBSITE_TAG: ${{ steps.branchTag.outputs.branchTag }} BACKEND_TAG: ${{ steps.branchTag.outputs.branchTag }} - - name: Run Playwright tests + - name: Run Playwright tests (all browsers) + if: github.ref == 'refs/heads/main' run: npm run e2e + - name: Run Playwright tests (chromium only) + if: github.ref != 'refs/heads/main' + run: npm run e2e:chromium + - uses: actions/upload-artifact@v6 if: ${{ !cancelled() }} with: diff --git a/website/package.json b/website/package.json index ccb5cf6c4..1d2a59d63 100644 --- a/website/package.json +++ b/website/package.json @@ -20,7 +20,8 @@ "test:headed": "vitest --browser.headless false", "test:browser": "vitest --project browser", "test:browser:headed": "vitest --project browser --browser.headless false", - "e2e": "playwright test" + "e2e": "playwright test", + "e2e:chromium": "playwright test --project=chromium" }, "dependencies": { "@astrojs/node": "^9.5.1", From 12820ec49a426096a656ed2cad9fde600680bff0 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 7 Jan 2026 08:22:08 +0100 Subject: [PATCH 15/26] chore(website): bump the minorandpatch group across 1 directory with 6 updates (#988) Bumps the minorandpatch group with 6 updates in the /website directory: | Package | From | To | | --- | --- | --- | | [@tanstack/react-query](https://github.com/TanStack/query/tree/HEAD/packages/react-query) | `5.90.12` | `5.90.15` | | [astro](https://github.com/withastro/astro/tree/HEAD/packages/astro) | `5.16.5` | `5.16.6` | | [@typescript-eslint/eslint-plugin](https://github.com/typescript-eslint/typescript-eslint/tree/HEAD/packages/eslint-plugin) | `8.50.0` | `8.51.0` | | [@typescript-eslint/parser](https://github.com/typescript-eslint/typescript-eslint/tree/HEAD/packages/parser) | `8.50.0` | `8.51.0` | | [msw](https://github.com/mswjs/msw) | `2.12.4` | `2.12.7` | | [typescript-eslint](https://github.com/typescript-eslint/typescript-eslint/tree/HEAD/packages/typescript-eslint) | `8.50.0` | `8.51.0` | Updates `@tanstack/react-query` from 5.90.12 to 5.90.15 - [Release notes](https://github.com/TanStack/query/releases) - [Changelog](https://github.com/TanStack/query/blob/main/packages/react-query/CHANGELOG.md) - [Commits](https://github.com/TanStack/query/commits/@tanstack/react-query@5.90.15/packages/react-query) Updates `astro` from 5.16.5 to 5.16.6 - [Release notes](https://github.com/withastro/astro/releases) - [Changelog](https://github.com/withastro/astro/blob/main/packages/astro/CHANGELOG.md) - [Commits](https://github.com/withastro/astro/commits/astro@5.16.6/packages/astro) Updates `@typescript-eslint/eslint-plugin` from 8.50.0 to 8.51.0 - [Release notes](https://github.com/typescript-eslint/typescript-eslint/releases) - [Changelog](https://github.com/typescript-eslint/typescript-eslint/blob/main/packages/eslint-plugin/CHANGELOG.md) - [Commits](https://github.com/typescript-eslint/typescript-eslint/commits/v8.51.0/packages/eslint-plugin) Updates `@typescript-eslint/parser` from 8.50.0 to 8.51.0 - [Release notes](https://github.com/typescript-eslint/typescript-eslint/releases) - [Changelog](https://github.com/typescript-eslint/typescript-eslint/blob/main/packages/parser/CHANGELOG.md) - [Commits](https://github.com/typescript-eslint/typescript-eslint/commits/v8.51.0/packages/parser) Updates `msw` from 2.12.4 to 2.12.7 - [Release notes](https://github.com/mswjs/msw/releases) - [Changelog](https://github.com/mswjs/msw/blob/main/CHANGELOG.md) - [Commits](https://github.com/mswjs/msw/compare/v2.12.4...v2.12.7) Updates `typescript-eslint` from 8.50.0 to 8.51.0 - [Release notes](https://github.com/typescript-eslint/typescript-eslint/releases) - [Changelog](https://github.com/typescript-eslint/typescript-eslint/blob/main/packages/typescript-eslint/CHANGELOG.md) - [Commits](https://github.com/typescript-eslint/typescript-eslint/commits/v8.51.0/packages/typescript-eslint) --- updated-dependencies: - dependency-name: "@tanstack/react-query" dependency-version: 5.90.15 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: minorandpatch - dependency-name: astro dependency-version: 5.16.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: minorandpatch - dependency-name: "@typescript-eslint/eslint-plugin" dependency-version: 8.51.0 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: minorandpatch - dependency-name: "@typescript-eslint/parser" dependency-version: 8.51.0 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: minorandpatch - dependency-name: msw dependency-version: 2.12.7 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: minorandpatch - dependency-name: typescript-eslint dependency-version: 8.51.0 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: minorandpatch ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- website/package-lock.json | 172 +++++++++++++++++++------------------- website/package.json | 12 +-- 2 files changed, 92 insertions(+), 92 deletions(-) diff --git a/website/package-lock.json b/website/package-lock.json index 54a935833..62b2c6c83 100644 --- a/website/package-lock.json +++ b/website/package-lock.json @@ -12,8 +12,8 @@ "@astrojs/node": "^9.5.1", "@auth/core": "^0.37.4", "@genspectrum/dashboard-components": "^1.12.0", - "@tanstack/react-query": "^5.90.12", - "astro": "^5.13.10", + "@tanstack/react-query": "^5.90.15", + "astro": "^5.16.6", "auth-astro": "^4.2.0", "axios": "^1.13.2", "cookie": "^1.1.1", @@ -48,8 +48,8 @@ "@types/react-dom": "^18.3.1", "@types/react-katex": "^3.0.4", "@types/topojson-specification": "^1.0.5", - "@typescript-eslint/eslint-plugin": "^8.50.0", - "@typescript-eslint/parser": "^8.50.0", + "@typescript-eslint/eslint-plugin": "^8.51.0", + "@typescript-eslint/parser": "^8.51.0", "@vitest/browser": "^3.2.4", "astro-eslint-parser": "^1.2.2", "daisyui": "^5.5.14", @@ -59,14 +59,14 @@ "eslint-plugin-import": "^2.32.0", "eslint-plugin-react": "^7.37.5", "eslint-plugin-react-hooks": "^5.2.0", - "msw": "^2.12.4", + "msw": "^2.12.7", "playwright": "^1.55.0", "prettier": "^3.7.4", "prettier-plugin-astro": "^0.14.1", "prettier-plugin-tailwindcss": "^0.7.2", "tailwindcss": "^4.0.9", "typescript": "^5.9.3", - "typescript-eslint": "^8.50.0", + "typescript-eslint": "^8.51.0", "vitest": "^3.2.4", "vitest-browser-react": "^1.0.1", "zod": "^3.25.74" @@ -3154,9 +3154,9 @@ } }, "node_modules/@tanstack/query-core": { - "version": "5.90.12", - "resolved": "https://registry.npmjs.org/@tanstack/query-core/-/query-core-5.90.12.tgz", - "integrity": "sha512-T1/8t5DhV/SisWjDnaiU2drl6ySvsHj1bHBCWNXd+/T+Hh1cf6JodyEYMd5sgwm+b/mETT4EV3H+zCVczCU5hg==", + "version": "5.90.15", + "resolved": "https://registry.npmjs.org/@tanstack/query-core/-/query-core-5.90.15.tgz", + "integrity": "sha512-mInIZNUZftbERE+/Hbtswfse49uUQwch46p+27gP9DWJL927UjnaWEF2t3RMOqBcXbfMdcNkPe06VyUIAZTV1g==", "license": "MIT", "funding": { "type": "github", @@ -3164,12 +3164,12 @@ } }, "node_modules/@tanstack/react-query": { - "version": "5.90.12", - "resolved": "https://registry.npmjs.org/@tanstack/react-query/-/react-query-5.90.12.tgz", - "integrity": "sha512-graRZspg7EoEaw0a8faiUASCyJrqjKPdqJ9EwuDRUF9mEYJ1YPczI9H+/agJ0mOJkPCJDk0lsz5QTrLZ/jQ2rg==", + "version": "5.90.15", + "resolved": "https://registry.npmjs.org/@tanstack/react-query/-/react-query-5.90.15.tgz", + "integrity": "sha512-uQvnDDcTOgJouNtAyrgRej+Azf0U5WDov3PXmHFUBc+t1INnAYhIlpZtCGNBLwCN41b43yO7dPNZu8xWkUFBwQ==", "license": "MIT", "dependencies": { - "@tanstack/query-core": "5.90.12" + "@tanstack/query-core": "5.90.15" }, "funding": { "type": "github", @@ -3514,20 +3514,20 @@ "license": "MIT" }, 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"sha512-rHNiVfTyKhzc0EjoXUBVGteNKBevdjOlVC6GlIRXpy+/3LHEIGRovnB5WPjcvmNODVQ1TNFnoa7wsGbd0V3epg==", + "version": "2.12.7", + "resolved": "https://registry.npmjs.org/msw/-/msw-2.12.7.tgz", + "integrity": "sha512-retd5i3xCZDVWMYjHEVuKTmhqY8lSsxujjVrZiGbbdoxxIBg5S7rCuYy/YQpfrTYIxpd/o0Kyb/3H+1udBMoYg==", "dev": true, "hasInstallScript": true, "license": "MIT", @@ -12855,9 +12855,9 @@ } }, "node_modules/ts-api-utils": { - "version": "2.1.0", - "resolved": "https://registry.npmjs.org/ts-api-utils/-/ts-api-utils-2.1.0.tgz", - "integrity": "sha512-CUgTZL1irw8u29bzrOD/nH85jqyc74D6SshFgujOIA7osm2Rz7dYH77agkx7H4FBNxDq7Cjf+IjaX/8zwFW+ZQ==", + "version": "2.3.0", + "resolved": "https://registry.npmjs.org/ts-api-utils/-/ts-api-utils-2.3.0.tgz", + "integrity": "sha512-6eg3Y9SF7SsAvGzRHQvvc1skDAhwI4YQ32ui1scxD1Ccr0G5qIIbUBT3pFTKX8kmWIQClHobtUdNuaBgwdfdWg==", "dev": true, "license": "MIT", "engines": { @@ -13054,16 +13054,16 @@ } }, "node_modules/typescript-eslint": { - "version": "8.50.0", - "resolved": "https://registry.npmjs.org/typescript-eslint/-/typescript-eslint-8.50.0.tgz", - "integrity": "sha512-Q1/6yNUmCpH94fbgMUMg2/BSAr/6U7GBk61kZTv1/asghQOWOjTlp9K8mixS5NcJmm2creY+UFfGeW/+OcA64A==", + "version": "8.51.0", + "resolved": "https://registry.npmjs.org/typescript-eslint/-/typescript-eslint-8.51.0.tgz", + "integrity": "sha512-jh8ZuM5oEh2PSdyQG9YAEM1TCGuWenLSuSUhf/irbVUNW9O5FhbFVONviN2TgMTBnUmyHv7E56rYnfLZK6TkiA==", "dev": true, "license": "MIT", "dependencies": { - "@typescript-eslint/eslint-plugin": "8.50.0", - "@typescript-eslint/parser": "8.50.0", - "@typescript-eslint/typescript-estree": "8.50.0", - "@typescript-eslint/utils": "8.50.0" + "@typescript-eslint/eslint-plugin": "8.51.0", + "@typescript-eslint/parser": "8.51.0", + "@typescript-eslint/typescript-estree": "8.51.0", + "@typescript-eslint/utils": "8.51.0" }, "engines": { "node": "^18.18.0 || ^20.9.0 || >=21.1.0" diff --git a/website/package.json b/website/package.json index 1d2a59d63..15fe68425 100644 --- a/website/package.json +++ b/website/package.json @@ -27,8 +27,8 @@ "@astrojs/node": "^9.5.1", "@auth/core": "^0.37.4", "@genspectrum/dashboard-components": "^1.12.0", - "@tanstack/react-query": "^5.90.12", - "astro": "^5.13.10", + "@tanstack/react-query": "^5.90.15", + "astro": "^5.16.6", "auth-astro": "^4.2.0", "axios": "^1.13.2", "cookie": "^1.1.1", @@ -63,8 +63,8 @@ "@types/react-dom": "^18.3.1", "@types/react-katex": "^3.0.4", "@types/topojson-specification": "^1.0.5", - "@typescript-eslint/eslint-plugin": "^8.50.0", - "@typescript-eslint/parser": "^8.50.0", + "@typescript-eslint/eslint-plugin": "^8.51.0", + "@typescript-eslint/parser": "^8.51.0", "@vitest/browser": "^3.2.4", "astro-eslint-parser": "^1.2.2", "daisyui": "^5.5.14", @@ -74,14 +74,14 @@ "eslint-plugin-import": "^2.32.0", "eslint-plugin-react": "^7.37.5", "eslint-plugin-react-hooks": "^5.2.0", - "msw": "^2.12.4", + "msw": "^2.12.7", "playwright": "^1.55.0", "prettier": "^3.7.4", "prettier-plugin-astro": "^0.14.1", "prettier-plugin-tailwindcss": "^0.7.2", "tailwindcss": "^4.0.9", "typescript": "^5.9.3", - "typescript-eslint": "^8.50.0", + "typescript-eslint": "^8.51.0", "vitest": "^3.2.4", "vitest-browser-react": "^1.0.1", "zod": "^3.25.74" From 8e7c7832d8603074831f5c883d96ba2cad21a09d Mon Sep 17 00:00:00 2001 From: Fabian Engelniederhammer <92720311+fengelniederhammer@users.noreply.github.com> Date: Wed, 7 Jan 2026 10:49:12 +0100 Subject: [PATCH 16/26] refactor(website): migrate "compare side-by-side" to React (#975) * refactor(website): migrate "compare side-by-side" to React * chore(website): add test * chore(website): fix lints * chore(website): fix type name --- .../GenericCompareSideBySideDataDisplay.tsx | 85 +++++++++++++++++++ .../GenericCompareSideBySidePage.astro | 72 +++------------- website/tests/CompareSideBySidePage.ts | 50 +++++++++++ website/tests/CompareToBaselinePage.ts | 8 +- website/tests/CompareVariantsPage.ts | 8 +- website/tests/ViewPage.ts | 13 ++- website/tests/compareSideBySide.spec.ts | 38 +++++++++ website/tests/e2e.fixture.ts | 5 ++ website/tests/helpers.ts | 2 + 9 files changed, 207 insertions(+), 74 deletions(-) create mode 100644 website/src/components/views/compareSideBySide/GenericCompareSideBySideDataDisplay.tsx create mode 100644 website/tests/CompareSideBySidePage.ts create mode 100644 website/tests/compareSideBySide.spec.ts diff --git a/website/src/components/views/compareSideBySide/GenericCompareSideBySideDataDisplay.tsx b/website/src/components/views/compareSideBySide/GenericCompareSideBySideDataDisplay.tsx new file mode 100644 index 000000000..4b84d3b47 --- /dev/null +++ b/website/src/components/views/compareSideBySide/GenericCompareSideBySideDataDisplay.tsx @@ -0,0 +1,85 @@ +import { type FC, useMemo } from 'react'; + +import type { OrganismsConfig } from '../../../config.ts'; +import { chooseGranularityBasedOnDateRange } from '../../../util/chooseGranularityBasedOnDateRange.ts'; +import { ComponentHeight } from '../../../views/OrganismConstants.ts'; +import type { DatasetAndVariantData } from '../../../views/View.ts'; +import { toLapisFilterWithoutVariant } from '../../../views/pageStateHandlers/toLapisFilterWithoutVariant.ts'; +import { type OrganismWithViewKey, Routing } from '../../../views/routing.ts'; +import { compareSideBySideViewKey } from '../../../views/viewKeys.ts'; +import { GsAggregate } from '../../genspectrum/GsAggregate.tsx'; +import { GsMutations } from '../../genspectrum/GsMutations.tsx'; +import { GsPrevalenceOverTime } from '../../genspectrum/GsPrevalenceOverTime.tsx'; + +export type GenericCompareSideBySideDataDisplayProps = { + organismViewKey: `${OrganismWithViewKey}.${typeof compareSideBySideViewKey}`; + organismsConfig: OrganismsConfig; + datasetAndVariantData: DatasetAndVariantData; + hideMutationComponents?: boolean; +}; + +export const GenericCompareSideBySideDataDisplay: FC = ({ + organismViewKey, + organismsConfig, + datasetAndVariantData, + hideMutationComponents, +}) => { + const view = useMemo( + () => new Routing(organismsConfig).getOrganismView(organismViewKey), + [organismsConfig, organismViewKey], + ); + + const { datasetFilter, variantFilter } = datasetAndVariantData; + + const datasetLapisFilter = toLapisFilterWithoutVariant(datasetFilter, view.organismConstants.additionalFilters); + const timeGranularity = chooseGranularityBasedOnDateRange({ + earliestDate: new Date(view.organismConstants.earliestDate), + dateRange: datasetFilter.dateFilters[view.organismConstants.mainDateField], + }); + const numeratorFilter = view.pageStateHandler.variantFilterToLapisFilter(datasetFilter, variantFilter); + + return ( + <> + + {hideMutationComponents !== true && ( + <> + + + + )} + + {view.organismConstants.aggregatedVisualizations.compareSideBySide.map(({ label, fields, views }) => ( + + ))} + + ); +}; diff --git a/website/src/components/views/compareSideBySide/GenericCompareSideBySidePage.astro b/website/src/components/views/compareSideBySide/GenericCompareSideBySidePage.astro index 81058b693..5fd6fcb31 100644 --- a/website/src/components/views/compareSideBySide/GenericCompareSideBySidePage.astro +++ b/website/src/components/views/compareSideBySide/GenericCompareSideBySidePage.astro @@ -1,16 +1,11 @@ --- +import { GenericCompareSideBySideDataDisplay } from './GenericCompareSideBySideDataDisplay.tsx'; import { toDownloadLink } from './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, type OrganismWithViewKey } from '../../../views/routing'; import { ServerSide } from '../../../views/serverSideRouting'; import { compareSideBySideViewKey } from '../../../views/viewKeys'; -import GsAggregate from '../../genspectrum/GsAggregate.astro'; -import GsMutations from '../../genspectrum/GsMutations.astro'; -import GsPrevalenceOverTime from '../../genspectrum/GsPrevalenceOverTime.astro'; import { CompareSideBySidePageStateSelector } from '../../pageStateSelectors/CompareSideBySidePageStateSelector'; import { CompareSideBySideSelectorFallback } from '../../pageStateSelectors/FallbackElement'; @@ -26,6 +21,8 @@ const view = ServerSide.routing.getOrganismView(organismViewKey); const pageState = view.pageStateHandler.parsePageStateFromUrl(Astro.url); +const organismConfig = getDashboardsConfig().dashboards.organisms; + const downloadLinks = [...pageState.filters.entries()].map(toDownloadLink(view.pageStateHandler, organism)); --- @@ -33,20 +30,7 @@ const downloadLinks = [...pageState.filters.entries()].map(toDownloadLink(view.p
{ - Array.from(pageState.filters).map(([id, { variantFilter, datasetFilter }]) => { - const datasetLapisFilter = toLapisFilterWithoutVariant( - datasetFilter, - view.organismConstants.additionalFilters, - ); - const timeGranularity = chooseGranularityBasedOnDateRange({ - earliestDate: new Date(view.organismConstants.earliestDate), - dateRange: datasetFilter.dateFilters[view.organismConstants.mainDateField], - }); - const numeratorFilter = view.pageStateHandler.variantFilterToLapisFilter( - datasetFilter, - variantFilter, - ); - + Array.from(pageState.filters).map(([id, datasetAndVariantData]) => { return (
@@ -63,7 +47,7 @@ const downloadLinks = [...pageState.filters.entries()].map(toDownloadLink(view.p
- - {!hideMutationComponents && ( - <> - - - - )} - - {view.organismConstants.aggregatedVisualizations.compareSideBySide.map( - ({ label, fields, views }) => ( - - ), - )}
); }) 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 index 9f41d2784..a5a091b3b 100644 --- a/website/tests/CompareToBaselinePage.ts +++ b/website/tests/CompareToBaselinePage.ts @@ -24,15 +24,11 @@ export class CompareToBaselinePage extends CompareVariantsPage { const { lineage, lineageFieldPlaceholder } = options; const lineageFieldLocator = this.page.getByPlaceholder(lineageFieldPlaceholder); - await lineageFieldLocator.first().fill(lineage); - - const selectedLineage = this.page.getByRole('option', { name: lineage, exact: false }); - await selectedLineage.first().click(); + await this.fillLineageField(lineageFieldLocator.first(), lineage); } if (options.mutation) { - await this.mutationField.first().fill(options.mutation); - await this.mutationField.first().press('Enter'); + 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/e2e.fixture.ts b/website/tests/e2e.fixture.ts index 6a655f331..3e4dbf6dc 100644 --- a/website/tests/e2e.fixture.ts +++ b/website/tests/e2e.fixture.ts @@ -1,5 +1,6 @@ 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'; @@ -8,6 +9,7 @@ type E2EFixture = { compareVariantsPage: CompareVariantsPage; sequencingEffortsPage: SequencingEffortsPage; compareToBaselinePage: CompareToBaselinePage; + compareSideBySidePage: CompareSideBySidePage; }; export const test = base.extend({ @@ -20,4 +22,7 @@ export const test = base.extend({ 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 2e3edba44..5dfda525f 100644 --- a/website/tests/helpers.ts +++ b/website/tests/helpers.ts @@ -8,9 +8,11 @@ export function organismsWithView(viewKey: ViewKey): Org 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' }, From b3cd25bf982d2118343cd13f4ab962fda0779226 Mon Sep 17 00:00:00 2001 From: Fabian Engelniederhammer <92720311+fengelniederhammer@users.noreply.github.com> Date: Wed, 7 Jan 2026 11:01:30 +0100 Subject: [PATCH 17/26] refactor(website): migrate covid "compare side-by-side" to React (#982) resolves #981 --- .../GenericCompareSideBySideDataDisplay.tsx | 10 ++ .../pages/covid/compare-side-by-side.astro | 130 +----------------- 2 files changed, 13 insertions(+), 127 deletions(-) diff --git a/website/src/components/views/compareSideBySide/GenericCompareSideBySideDataDisplay.tsx b/website/src/components/views/compareSideBySide/GenericCompareSideBySideDataDisplay.tsx index 4b84d3b47..53921b476 100644 --- a/website/src/components/views/compareSideBySide/GenericCompareSideBySideDataDisplay.tsx +++ b/website/src/components/views/compareSideBySide/GenericCompareSideBySideDataDisplay.tsx @@ -1,6 +1,7 @@ import { type FC, useMemo } from 'react'; import type { OrganismsConfig } from '../../../config.ts'; +import { Organisms } from '../../../types/Organism.ts'; import { chooseGranularityBasedOnDateRange } from '../../../util/chooseGranularityBasedOnDateRange.ts'; import { ComponentHeight } from '../../../views/OrganismConstants.ts'; import type { DatasetAndVariantData } from '../../../views/View.ts'; @@ -10,6 +11,7 @@ import { compareSideBySideViewKey } from '../../../views/viewKeys.ts'; import { GsAggregate } from '../../genspectrum/GsAggregate.tsx'; import { GsMutations } from '../../genspectrum/GsMutations.tsx'; import { GsPrevalenceOverTime } from '../../genspectrum/GsPrevalenceOverTime.tsx'; +import { GsRelativeGrowthAdvantage } from '../../genspectrum/GsRelativeGrowthAdvantage.tsx'; export type GenericCompareSideBySideDataDisplayProps = { organismViewKey: `${OrganismWithViewKey}.${typeof compareSideBySideViewKey}`; @@ -53,6 +55,14 @@ export const GenericCompareSideBySideDataDisplay: FC + {view.organismConstants.organism === Organisms.covid && ( + + )} {hideMutationComponents !== true && ( <> - -
- { - 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 ( -
-
- {pageState.filters.size > 1 && ( - - Remove column - - )} - - - -
- - - - - - {view.organismConstants.aggregatedVisualizations.compareSideBySide.map( - ({ label, fields, views }) => ( - - ), - )} -
- ); - }) - } - - Add column - -
- - + From bba733a36965c37ff356c97c4fc4c1f1aa2c595c Mon Sep 17 00:00:00 2001 From: Felix Hennig Date: Wed, 7 Jan 2026 12:34:01 +0000 Subject: [PATCH 18/26] feat(website): display clinical sequence count on variant explorer, with warning for small numbers (#980) --- .../wasap/filters/VariantExplorerFilter.tsx | 11 ++- .../src/components/views/wasap/WasapPage.tsx | 94 +++++++++++++++++-- .../views/wasap/useWasapPageData.ts | 26 ++--- .../components/views/wasap/wasapPageConfig.ts | 12 +++ website/src/types/wastewaterConfig.ts | 2 + .../WasapPageStateHandler.spec.ts | 1 + 6 files changed, 120 insertions(+), 26 deletions(-) diff --git a/website/src/components/pageStateSelectors/wasap/filters/VariantExplorerFilter.tsx b/website/src/components/pageStateSelectors/wasap/filters/VariantExplorerFilter.tsx index 1186e83d8..635f01fb7 100644 --- a/website/src/components/pageStateSelectors/wasap/filters/VariantExplorerFilter.tsx +++ b/website/src/components/pageStateSelectors/wasap/filters/VariantExplorerFilter.tsx @@ -2,6 +2,7 @@ import { Inset } from '../../../../styles/Inset'; import { GsLineageFilter } from '../../../genspectrum/GsLineageFilter'; import { VARIANT_TIME_FRAME, + variantTimeFrameLabel, type VariantTimeFrame, type WasapVariantFilter, } from '../../../views/wasap/wasapPageConfig'; @@ -80,9 +81,13 @@ export function VariantExplorerFilter({ value={pageState.timeFrame} onChange={(e) => setPageState({ ...pageState, timeFrame: e.target.value as VariantTimeFrame })} > - - - + + + diff --git a/website/src/components/views/wasap/WasapPage.tsx b/website/src/components/views/wasap/WasapPage.tsx index 52f94c8c7..70cc2d2f5 100644 --- a/website/src/components/views/wasap/WasapPage.tsx +++ b/website/src/components/views/wasap/WasapPage.tsx @@ -4,8 +4,13 @@ import { useMemo } from 'react'; import { type FC } from 'react'; import { toMutationAnnotations } from './resistanceMutations'; -import { useWasapPageData } from './useWasapPageData'; -import type { WasapAnalysisFilter, WasapPageConfig } from './wasapPageConfig'; +import { getLapisFilterForTimeFrame, useWasapPageData } from './useWasapPageData'; +import { + variantTimeFrameLabel, + type WasapAnalysisFilter, + type WasapPageConfig, + type WasapVariantFilter, +} from './wasapPageConfig'; import { getDateRange } from '../../../lapis/getDateRange'; import { getTotalCount } from '../../../lapis/getTotalCount'; import { wastewaterOrganismConfigs, type WastewaterOrganismName } from '../../../types/wastewaterConfig'; @@ -95,6 +100,15 @@ export const WasapPageInner: FC = ({ 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 ( +
+
+
Clinical sequences for {analysis.variant}
+
+ {isPending ? ( + '…' + ) : isError ? ( + 'Error' + ) : isHighlighted ? ( + {data.toLocaleString('en-us')} + ) : ( + data.toLocaleString('en-us') + )} +
+
{isPending ? 'Loading …' : isError ? error.message : message}
+
+
+ ); +}; + +const WasapStats = ({ config }: { config: WasapPageConfig }) => ( +
+ + +
+); + const TotalCount = ({ config }: { config: WasapPageConfig }) => { const { data, isPending, isError, error } = useQuery({ queryKey: ['aggregatedCount'], @@ -139,7 +218,9 @@ const TotalCount = ({ config }: { config: WasapPageConfig }) => { 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 01082e8a7..309a169f9 100644 --- a/website/src/components/views/wasap/useWasapPageData.ts +++ b/website/src/components/views/wasap/useWasapPageData.ts @@ -6,6 +6,18 @@ import type { VariantTimeFrame, WasapAnalysisFilter, WasapPageConfig } from './w 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'; }; @@ -99,7 +111,7 @@ async function fetchMutationSelection( } } -function getLapisFilterForTimeFrame(timeFrame: VariantTimeFrame, dateFieldName: string): LapisFilter { +export function getLapisFilterForTimeFrame(timeFrame: VariantTimeFrame, dateFieldName: string): LapisFilter { let fromDate = undefined; switch (timeFrame) { case 'all': @@ -161,15 +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 52c98df41..1ff438119 100644 --- a/website/src/components/views/wasap/wasapPageConfig.ts +++ b/website/src/components/views/wasap/wasapPageConfig.ts @@ -77,6 +77,7 @@ type VariantAnalysisModeConfig = filterDefaults: { variant: WasapVariantFilter; }; + clinicalSequenceCountWarningThreshold: number; }; type ResistanceAnalysisModeConfig = @@ -166,6 +167,17 @@ export const VARIANT_TIME_FRAME = { 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; diff --git a/website/src/types/wastewaterConfig.ts b/website/src/types/wastewaterConfig.ts index 3b9ac3c0b..1c95f9cbd 100644 --- a/website/src/types/wastewaterConfig.ts +++ b/website/src/types/wastewaterConfig.ts @@ -40,6 +40,7 @@ export const wastewaterOrganismConfigs: Record Date: Thu, 8 Jan 2026 08:37:35 +0100 Subject: [PATCH 19/26] refactor(website): refactor footer to pull "download data" button closer to React-rendered content (#978) * refactor(website): refactor footer to pull "download data" button closer to React-rendered content so that in a next step, that part of the footer can actually be rendered in React (since it depends on the page state) resolves #977 * refactor(website): move it back --- .../GenericCompareSideBySidePage.astro | 98 +++++++++---------- .../layouts/OrganismPage/DataPageLayout.astro | 46 +++++---- .../OrganismPage/OrganismViewPageLayout.astro | 7 +- .../SingleVariantOrganismPageLayout.astro | 16 +-- website/src/layouts/base/BaseLayout.astro | 5 +- website/src/layouts/base/footer/Footer.astro | 4 - .../layouts/base/footer/SecondaryFooter.astro | 7 -- website/src/pages/index.astro | 4 +- 8 files changed, 89 insertions(+), 98 deletions(-) delete mode 100644 website/src/layouts/base/footer/SecondaryFooter.astro diff --git a/website/src/components/views/compareSideBySide/GenericCompareSideBySidePage.astro b/website/src/components/views/compareSideBySide/GenericCompareSideBySidePage.astro index 5fd6fcb31..fe397ea9d 100644 --- a/website/src/components/views/compareSideBySide/GenericCompareSideBySidePage.astro +++ b/website/src/components/views/compareSideBySide/GenericCompareSideBySidePage.astro @@ -1,7 +1,7 @@ --- import { GenericCompareSideBySideDataDisplay } from './GenericCompareSideBySideDataDisplay.tsx'; import { toDownloadLink } from './toDownloadLink'; -import { isStaging, getDashboardsConfig, getLapisUrl } from '../../../config'; +import { isStaging, getDashboardsConfig } from '../../../config'; import OrganismViewPageLayout from '../../../layouts/OrganismPage/OrganismViewPageLayout.astro'; import { type OrganismViewKey, type OrganismWithViewKey } from '../../../views/routing'; import { ServerSide } from '../../../views/serverSideRouting'; @@ -27,56 +27,54 @@ const downloadLinks = [...pageState.filters.entries()].map(toDownloadLink(view.p --- - -
- { - Array.from(pageState.filters).map(([id, datasetAndVariantData]) => { - return ( -
-
- {pageState.filters.size > 1 && ( - - Remove column - - )} - + { + Array.from(pageState.filters).map(([id, datasetAndVariantData]) => { + return ( +
+
+ {pageState.filters.size > 1 && ( + - - -
- - + )} + + organismViewKey={organismViewKey} + enableAdvancedQueryFilter={isStaging()} + client:only='react' + > + +
- ); - }) - } - - Add column - -
- + + +
+ ); + }) + } + + Add column + +
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/index.astro b/website/src/pages/index.astro index f7c21db3e..be85c87ee 100644 --- a/website/src/pages/index.astro +++ b/website/src/pages/index.astro @@ -117,5 +117,7 @@ import { Page } from '../types/pages';
- +
+ +
From 12abdce27a6ef1cf5ec8766ce56f6c4d35db5994 Mon Sep 17 00:00:00 2001 From: Felix Hennig Date: Mon, 12 Jan 2026 13:03:37 +0000 Subject: [PATCH 20/26] fix(website): fix untracked mutations (#992) --- website/src/components/views/wasap/useWasapPageData.ts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/website/src/components/views/wasap/useWasapPageData.ts b/website/src/components/views/wasap/useWasapPageData.ts index 309a169f9..e9a2531db 100644 --- a/website/src/components/views/wasap/useWasapPageData.ts +++ b/website/src/components/views/wasap/useWasapPageData.ts @@ -94,7 +94,7 @@ async function fetchMutationSelection( config.clinicalLapis.lapisBaseUrl, analysis.sequenceType, { - [config.clinicalLapis.lapisBaseUrl]: variant, + [config.clinicalLapis.lineageField]: variant, }, 0.8, 9, From d7f6010a33a7e56accdf6e6978e31bb37eaecfb8 Mon Sep 17 00:00:00 2001 From: Fabian Engelniederhammer <92720311+fengelniederhammer@users.noreply.github.com> Date: Tue, 13 Jan 2026 08:20:13 +0100 Subject: [PATCH 21/26] refactor(website): render the whole layout in React (#983) * 979 also render the layouts in React * 979 fix stuff * 979 fix test --- ...sUnreachableWrapperClient.browser.spec.tsx | 53 ++++---- .../LapisUnreachableWrapperClient.tsx | 7 +- .../pageStateSelectors/FallbackElement.tsx | 38 ------ .../CovidSingleVariantReactPage.tsx | 78 ++++++++++++ .../GenericAnalyseSingleVariantReactPage.tsx | 76 +++++++++++ .../GenericAnalyzeSingleVariantPage.astro | 68 ++-------- .../GenericCompareSideBySidePage.astro | 82 +++--------- .../GenericCompareSideBySideReactPage.tsx | 87 +++++++++++++ .../GenericCompareToBaselinePage.astro | 55 ++------ .../GenericCompareToBaselineReactPage.tsx | 63 ++++++++++ .../GenericCompareVariantsPage.astro | 54 ++------ .../GenericCompareVariantsReactPage.tsx | 63 ++++++++++ .../GenericSequencingEffortsPage.astro | 55 ++------ .../GenericSequencingEffortsReactPage.tsx | 61 +++++++++ .../src/components/views/wasap/Wasap.astro | 28 +---- .../src/components/views/wasap/WasapPage.tsx | 118 ++++++++++-------- website/src/lapis/getLastUpdatedDate.spec.ts | 4 +- website/src/lapis/getLastUpdatedDate.ts | 10 +- .../AccessionsDownloadButton.astro | 53 -------- .../OrganismPage/AccessionsDownloadButton.tsx | 63 ++++++++++ .../layouts/OrganismPage/DataPageLayout.astro | 48 ------- .../layouts/OrganismPage/DataPageLayout.tsx | 50 ++++++++ .../OrganismPage/LastUpdatedInfo.astro | 13 -- .../layouts/OrganismPage/LastUpdatedInfo.tsx | 18 +++ .../OrganismPage/OrganismViewPageLayout.astro | 33 ----- .../OrganismPage/OrganismViewPageLayout.tsx | 34 +++++ .../SingleVariantOrganismPageLayout.astro | 25 ---- .../SingleVariantOrganismPageLayout.tsx | 37 ++++++ .../src/layouts/base/footer/DataInfo.astro | 26 ---- website/src/layouts/base/footer/DataInfo.tsx | 38 ++++++ .../layouts/base/footer/DataOriginLink.astro | 12 -- website/src/pages/covid/single-variant.astro | 76 ++--------- website/src/pages/index.astro | 2 +- website/src/pages/swiss-wastewater/flu.astro | 90 ++++++------- website/src/pages/swiss-wastewater/rsv.astro | 92 +++++++------- 35 files changed, 942 insertions(+), 768 deletions(-) delete mode 100644 website/src/components/pageStateSelectors/FallbackElement.tsx create mode 100644 website/src/components/views/analyzeSingleVariant/CovidSingleVariantReactPage.tsx create mode 100644 website/src/components/views/analyzeSingleVariant/GenericAnalyseSingleVariantReactPage.tsx create mode 100644 website/src/components/views/compareSideBySide/GenericCompareSideBySideReactPage.tsx create mode 100644 website/src/components/views/compareToBaseline/GenericCompareToBaselineReactPage.tsx create mode 100644 website/src/components/views/compareVariants/GenericCompareVariantsReactPage.tsx create mode 100644 website/src/components/views/sequencingEfforts/GenericSequencingEffortsReactPage.tsx delete mode 100644 website/src/layouts/OrganismPage/AccessionsDownloadButton.astro create mode 100644 website/src/layouts/OrganismPage/AccessionsDownloadButton.tsx delete mode 100644 website/src/layouts/OrganismPage/DataPageLayout.astro create mode 100644 website/src/layouts/OrganismPage/DataPageLayout.tsx delete mode 100644 website/src/layouts/OrganismPage/LastUpdatedInfo.astro create mode 100644 website/src/layouts/OrganismPage/LastUpdatedInfo.tsx delete mode 100644 website/src/layouts/OrganismPage/OrganismViewPageLayout.astro create mode 100644 website/src/layouts/OrganismPage/OrganismViewPageLayout.tsx delete mode 100644 website/src/layouts/OrganismPage/SingleVariantOrganismPageLayout.astro create mode 100644 website/src/layouts/OrganismPage/SingleVariantOrganismPageLayout.tsx delete mode 100644 website/src/layouts/base/footer/DataInfo.astro create mode 100644 website/src/layouts/base/footer/DataInfo.tsx delete mode 100644 website/src/layouts/base/footer/DataOriginLink.astro diff --git a/website/src/components/LapisUnreachableWrapperClient.browser.spec.tsx b/website/src/components/LapisUnreachableWrapperClient.browser.spec.tsx index 3108cf7b0..c33f73371 100644 --- a/website/src/components/LapisUnreachableWrapperClient.browser.spec.tsx +++ b/website/src/components/LapisUnreachableWrapperClient.browser.spec.tsx @@ -1,31 +1,28 @@ +import { QueryClient, QueryClientProvider } from '@tanstack/react-query'; import { describe, expect } from 'vitest'; import { render } from 'vitest-browser-react'; -import LapisUnreachableWrapperClient from './LapisUnreachableWrapperClient'; +import { LapisUnreachableWrapperClient } from './LapisUnreachableWrapperClient'; import { DUMMY_LAPIS_URL } from '../../routeMocker'; import { it } from '../../test-extend'; +const queryClient = new QueryClient(); + describe('LapisUnreachableWrapperClient', () => { it('displays children when LAPIS is reachable', async ({ routeMockers: { lapis } }) => { lapis.mockPostAggregated({}, { data: [{ count: 100 }] }); - const { getByText } = render( - -
Content is visible
- , - ); + const content = 'Content is visible'; + + const { getByText } = renderWithContent(content); - await expect.element(getByText('Content is visible')).toBeVisible(); + await expect.element(getByText(content)).toBeVisible(); }); it('displays error message when LAPIS is unreachable', async ({ routeMockers: { lapis } }) => { lapis.mockLapisDown(); - const { getByText } = render( - -
Content is visible
- , - ); + const { getByText } = renderWithContent('Content is visible'); await expect.element(getByText('Data Source Unreachable')).toBeVisible(); await expect.element(getByText('Unable to connect to the data source')).toBeVisible(); @@ -34,23 +31,17 @@ describe('LapisUnreachableWrapperClient', () => { it('does not display children when LAPIS is unreachable', async ({ routeMockers: { lapis } }) => { lapis.mockLapisDown(); - const { getByText } = render( - -
Content should not be visible
- , - ); + const content = 'Content is visible'; - await expect.poll(() => getByText('Content should not be visible').query()).not.toBeInTheDocument(); + const { getByText } = renderWithContent(content); + + await expect.poll(() => getByText(content).query()).not.toBeInTheDocument(); }); it('displays error when LAPIS returns invalid response', async ({ routeMockers: { lapis } }) => { lapis.mockPostAggregated({}, { data: [] }, 200); - const { getByText } = render( - -
Content is visible
- , - ); + const { getByText } = renderWithContent('Content is visible'); await expect.element(getByText('Data Source Unreachable')).toBeVisible(); }); @@ -58,12 +49,18 @@ describe('LapisUnreachableWrapperClient', () => { it('displays error when LAPIS returns 500', async ({ routeMockers: { lapis } }) => { lapis.mockPostAggregated({}, { data: [{ count: 100 }] }, 500); - const { getByText } = render( - -
Content is visible
- , - ); + const { getByText } = renderWithContent('Content is visible'); await expect.element(getByText('Data Source Unreachable')).toBeVisible(); }); }); + +function renderWithContent(content: string) { + return render( + + +
{content}
+ + , + ); +} diff --git a/website/src/components/LapisUnreachableWrapperClient.tsx b/website/src/components/LapisUnreachableWrapperClient.tsx index 18307c761..ddec59b3a 100644 --- a/website/src/components/LapisUnreachableWrapperClient.tsx +++ b/website/src/components/LapisUnreachableWrapperClient.tsx @@ -2,14 +2,13 @@ import { useQuery } from '@tanstack/react-query'; import { type FC, type ReactNode } from 'react'; import { checkLapisHealth } from '../lapis/checkLapisHealth'; -import { withQueryProvider } from './subscriptions/backendApi/withQueryProvider'; type LapisUnreachableWrapperClientProps = { lapisUrl: string; children: ReactNode; }; -const LapisUnreachableWrapperClientInner: FC = ({ lapisUrl, children }) => { +export const LapisUnreachableWrapperClient: FC = ({ lapisUrl, children }) => { const { data: isReachable, isLoading } = useQuery({ queryKey: ['lapis-reachable', lapisUrl], queryFn: () => checkLapisHealth(lapisUrl), @@ -37,7 +36,3 @@ const LapisUnreachableWrapperClientInner: FC return <>{children}; }; - -const LapisUnreachableWrapperClient = withQueryProvider(LapisUnreachableWrapperClientInner); - -export default LapisUnreachableWrapperClient; diff --git a/website/src/components/pageStateSelectors/FallbackElement.tsx b/website/src/components/pageStateSelectors/FallbackElement.tsx deleted file mode 100644 index ed5d3090e..000000000 --- a/website/src/components/pageStateSelectors/FallbackElement.tsx +++ /dev/null @@ -1,38 +0,0 @@ -export function SequencingEffortsSelectorFallback() { - return
; -} - -export function AnalyzeSingleVariantSelectorFallback() { - return
; -} - -export function CompareSideBySideSelectorFallback({ numFilters }: { numFilters: number }) { - return ( -
- {numFilters > 2 &&
} - {numFilters <= 2 &&
} -
- ); -} - -export function CompareToBaselineSelectorFallback({ numFilters }: { numFilters: number }) { - return ( - <> -
- {Array.from({ length: numFilters }).map((_, index) => ( -
- ))} - - ); -} - -export function CompareVariantsSelectorFallback({ numFilters }: { numFilters: number }) { - return ( - <> -
- {Array.from({ length: numFilters }).map((_, index) => ( -
- ))} - - ); -} diff --git a/website/src/components/views/analyzeSingleVariant/CovidSingleVariantReactPage.tsx b/website/src/components/views/analyzeSingleVariant/CovidSingleVariantReactPage.tsx new file mode 100644 index 000000000..35b12bad5 --- /dev/null +++ b/website/src/components/views/analyzeSingleVariant/CovidSingleVariantReactPage.tsx @@ -0,0 +1,78 @@ +import { type FC, useMemo } from 'react'; + +import { CollectionsList } from './CollectionsList.tsx'; +import { CovidSingleVariantDataDisplay } from './CovidSingleVariantDataDisplay.tsx'; +import type { OrganismsConfig } from '../../../config.ts'; +import { SingleVariantOrganismPageLayout } from '../../../layouts/OrganismPage/SingleVariantOrganismPageLayout.tsx'; +import { hasOnlyUndefinedValues } from '../../../util/hasOnlyUndefinedValues.ts'; +import { toDisplayName } from '../../../views/pageStateHandlers/PageStateHandler.ts'; +import { type OrganismViewKey, Routing } from '../../../views/routing.ts'; +import { SelectorHeadline } from '../../pageStateSelectors/SelectorHeadline.tsx'; +import { SingleVariantPageStateSelector } from '../../pageStateSelectors/SingleVariantPageStateSelector.tsx'; +import { sanitizeForFilename } from '../compareSideBySide/toDownloadLink.ts'; + +export type CovidSingleVariantReactPageProps = { + organismsConfig: OrganismsConfig; + isStaging: boolean; +}; + +export const CovidSingleVariantReactPage: FC = ({ organismsConfig, isStaging }) => { + const organismViewKey: OrganismViewKey = 'covid.singleVariantView'; + const view = useMemo(() => new Routing(organismsConfig).getOrganismView(organismViewKey), [organismsConfig]); + + const pageState = view.pageStateHandler.parsePageStateFromUrl(new URL(window.location.href)); + + const variantFilter = view.pageStateHandler.toLapisFilter(pageState); + + const noVariantSelected = hasOnlyUndefinedValues(pageState.variantFilter); + + const displayName = toDisplayName(pageState.variantFilter); + const downloadLinks = noVariantSelected + ? [ + { + label: 'Download all accessions', + filter: variantFilter, + downloadFileBasename: `${view.organismConstants.organism}_accessions`, + }, + ] + : [ + { + label: `Download accessions of ${displayName}`, + filter: variantFilter, + downloadFileBasename: `${view.organismConstants.organism}_${sanitizeForFilename(displayName)}_accessions`, + }, + ]; + + return ( + + +
+
+ Collections + +
+ + } + dataDisplay={ + + } + /> + ); +}; diff --git a/website/src/components/views/analyzeSingleVariant/GenericAnalyseSingleVariantReactPage.tsx b/website/src/components/views/analyzeSingleVariant/GenericAnalyseSingleVariantReactPage.tsx new file mode 100644 index 000000000..3a9c770f8 --- /dev/null +++ b/website/src/components/views/analyzeSingleVariant/GenericAnalyseSingleVariantReactPage.tsx @@ -0,0 +1,76 @@ +import { type FC, useMemo } from 'react'; + +import { GenericAnalyseSingleVariantDataDisplay } from './GenericAnalyseSingleVariantDataDisplay'; +import { type OrganismsConfig } from '../../../config'; +import { SingleVariantOrganismPageLayout } from '../../../layouts/OrganismPage/SingleVariantOrganismPageLayout.tsx'; +import { Organisms } from '../../../types/Organism'; +import { hasOnlyUndefinedValues } from '../../../util/hasOnlyUndefinedValues'; +import { toDisplayName } from '../../../views/pageStateHandlers/PageStateHandler'; +import { type OrganismViewKey, type OrganismWithViewKey, Routing } from '../../../views/routing'; +import { singleVariantViewKey } from '../../../views/viewKeys'; +import { SingleVariantPageStateSelector } from '../../pageStateSelectors/SingleVariantPageStateSelector'; +import { sanitizeForFilename } from '../compareSideBySide/toDownloadLink'; + +export type GenericAnalyseSingleVariantReactPageProps = { + organism: Exclude, typeof Organisms.covid>; + organismsConfig: OrganismsConfig; + isStaging: boolean; +}; + +export const GenericAnalyseSingleVariantReactPage: FC = ({ + organism, + organismsConfig, + isStaging, +}) => { + const organismViewKey = `${organism}.${singleVariantViewKey}` satisfies OrganismViewKey; + const view = useMemo( + () => new Routing(organismsConfig).getOrganismView(organismViewKey), + [organismsConfig, organismViewKey], + ); + + const pageState = view.pageStateHandler.parsePageStateFromUrl(new URL(window.location.href)); + + const variantLapisFilter = view.pageStateHandler.toLapisFilter(pageState); + + const noVariantSelected = hasOnlyUndefinedValues(pageState.variantFilter); + + const displayName = toDisplayName(pageState.variantFilter); + const downloadLinks = noVariantSelected + ? [ + { + label: 'Download all accessions', + filter: variantLapisFilter, + downloadFileBasename: `${view.organismConstants.organism}_accessions`, + }, + ] + : [ + { + label: `Download accessions of "${displayName}"`, + filter: variantLapisFilter, + downloadFileBasename: `${organism}_${sanitizeForFilename(displayName)}_accessions`, + }, + ]; + + return ( + + } + dataDisplay={ + + } + /> + ); +}; diff --git a/website/src/components/views/analyzeSingleVariant/GenericAnalyzeSingleVariantPage.astro b/website/src/components/views/analyzeSingleVariant/GenericAnalyzeSingleVariantPage.astro index 256b7079a..83fe543bf 100644 --- a/website/src/components/views/analyzeSingleVariant/GenericAnalyzeSingleVariantPage.astro +++ b/website/src/components/views/analyzeSingleVariant/GenericAnalyzeSingleVariantPage.astro @@ -1,70 +1,26 @@ --- -import { GenericAnalyseSingleVariantDataDisplay } from './GenericAnalyseSingleVariantDataDisplay'; +import { GenericAnalyseSingleVariantReactPage } from './GenericAnalyseSingleVariantReactPage'; import { isStaging, getDashboardsConfig } from '../../../config'; -import SingleVariantOrganismPageLayout from '../../../layouts/OrganismPage/SingleVariantOrganismPageLayout.astro'; +import BaseLayout from '../../../layouts/base/BaseLayout.astro'; import { Organisms } from '../../../types/Organism'; -import { hasOnlyUndefinedValues } from '../../../util/hasOnlyUndefinedValues'; -import { toDisplayName } from '../../../views/pageStateHandlers/PageStateHandler'; -import { type OrganismViewKey, type OrganismWithViewKey } from '../../../views/routing'; +import { type OrganismWithViewKey } from '../../../views/routing'; import { ServerSide } from '../../../views/serverSideRouting'; import { singleVariantViewKey } from '../../../views/viewKeys'; -import { AnalyzeSingleVariantSelectorFallback } from '../../pageStateSelectors/FallbackElement'; -import { SingleVariantPageStateSelector } from '../../pageStateSelectors/SingleVariantPageStateSelector'; -import { sanitizeForFilename } from '../compareSideBySide/toDownloadLink'; -type OrganismViewCompareVariant = OrganismWithViewKey; interface Props { - organism: Exclude; + organism: Exclude, typeof Organisms.covid>; } const { organism } = Astro.props; -const organismViewKey = `${organism}.${singleVariantViewKey}` satisfies OrganismViewKey; -const view = ServerSide.routing.getOrganismView(organismViewKey); -const pageState = view.pageStateHandler.parsePageStateFromUrl(Astro.url); - -const variantLapisFilter = view.pageStateHandler.toLapisFilter(pageState); - -const noVariantSelected = hasOnlyUndefinedValues(pageState.variantFilter); - -const organismConfig = getDashboardsConfig().dashboards.organisms; - -const displayName = toDisplayName(pageState.variantFilter); -const downloadLinks = noVariantSelected - ? [ - { - label: 'Download all accessions', - filter: variantLapisFilter, - downloadFileBasename: `${view.organismConstants.organism}_accessions`, - }, - ] - : [ - { - label: `Download accessions of "${displayName}"`, - filter: variantLapisFilter, - downloadFileBasename: `${organism}_${sanitizeForFilename(displayName)}_accessions`, - }, - ]; +const view = ServerSide.routing.getOrganismView(`${organism}.${singleVariantViewKey}`); --- - - + - - - -
- -
- + /> + diff --git a/website/src/components/views/compareSideBySide/GenericCompareSideBySidePage.astro b/website/src/components/views/compareSideBySide/GenericCompareSideBySidePage.astro index fe397ea9d..e6216e72e 100644 --- a/website/src/components/views/compareSideBySide/GenericCompareSideBySidePage.astro +++ b/website/src/components/views/compareSideBySide/GenericCompareSideBySidePage.astro @@ -1,80 +1,28 @@ --- -import { GenericCompareSideBySideDataDisplay } from './GenericCompareSideBySideDataDisplay.tsx'; -import { toDownloadLink } from './toDownloadLink'; +import { GenericCompareSideBySideReactPage } from './GenericCompareSideBySideReactPage'; import { isStaging, getDashboardsConfig } from '../../../config'; -import OrganismViewPageLayout from '../../../layouts/OrganismPage/OrganismViewPageLayout.astro'; -import { type OrganismViewKey, type OrganismWithViewKey } from '../../../views/routing'; +import BaseLayout from '../../../layouts/base/BaseLayout.astro'; +import { type OrganismWithViewKey } from '../../../views/routing'; import { ServerSide } from '../../../views/serverSideRouting'; import { compareSideBySideViewKey } from '../../../views/viewKeys'; -import { CompareSideBySidePageStateSelector } from '../../pageStateSelectors/CompareSideBySidePageStateSelector'; -import { CompareSideBySideSelectorFallback } from '../../pageStateSelectors/FallbackElement'; -type OrganismViewCompareVariant = OrganismWithViewKey; interface Props { - organism: OrganismViewCompareVariant; + organism: OrganismWithViewKey; hideMutationComponents?: boolean; } const { organism, hideMutationComponents } = Astro.props; -const organismViewKey = `${organism}.${compareSideBySideViewKey}` satisfies OrganismViewKey; -const view = ServerSide.routing.getOrganismView(organismViewKey); -const pageState = view.pageStateHandler.parsePageStateFromUrl(Astro.url); - -const organismConfig = getDashboardsConfig().dashboards.organisms; - -const downloadLinks = [...pageState.filters.entries()].map(toDownloadLink(view.pageStateHandler, organism)); +const view = ServerSide.routing.getOrganismView(`${organism}.${compareSideBySideViewKey}`); +const organismsConfig = getDashboardsConfig().dashboards.organisms; --- - -
- { - Array.from(pageState.filters).map(([id, datasetAndVariantData]) => { - return ( -
-
- {pageState.filters.size > 1 && ( - - Remove column - - )} - - - -
- - -
- ); - }) - } - - Add column - -
- + + + diff --git a/website/src/components/views/compareSideBySide/GenericCompareSideBySideReactPage.tsx b/website/src/components/views/compareSideBySide/GenericCompareSideBySideReactPage.tsx new file mode 100644 index 000000000..20e72eede --- /dev/null +++ b/website/src/components/views/compareSideBySide/GenericCompareSideBySideReactPage.tsx @@ -0,0 +1,87 @@ +import { type FC, useMemo } from 'react'; + +import { GenericCompareSideBySideDataDisplay } from './GenericCompareSideBySideDataDisplay.tsx'; +import { toDownloadLink } from './toDownloadLink'; +import { type OrganismsConfig } from '../../../config'; +import { OrganismViewPageLayout } from '../../../layouts/OrganismPage/OrganismViewPageLayout.tsx'; +import { type OrganismViewKey, type OrganismWithViewKey, Routing } from '../../../views/routing'; +import { compareSideBySideViewKey } from '../../../views/viewKeys'; +import { CompareSideBySidePageStateSelector } from '../../pageStateSelectors/CompareSideBySidePageStateSelector'; + +export type GenericCompareSideBySideReactPageProps = { + organism: OrganismWithViewKey; + hideMutationComponents?: boolean; + organismsConfig: OrganismsConfig; + isStaging: boolean; +}; + +export const GenericCompareSideBySideReactPage: FC = ({ + organism, + hideMutationComponents, + organismsConfig, + isStaging, +}) => { + const organismViewKey = `${organism}.${compareSideBySideViewKey}` satisfies OrganismViewKey; + + const view = useMemo( + () => new Routing(organismsConfig).getOrganismView(organismViewKey), + [organismsConfig, organismViewKey], + ); + + const pageState = view.pageStateHandler.parsePageStateFromUrl(new URL(window.location.href)); + + const downloadLinks = [...pageState.filters.entries()].map(toDownloadLink(view.pageStateHandler, organism)); + + return ( + +
+ {Array.from(pageState.filters).map(([id, datasetAndVariantData]) => { + return ( +
+
+ {pageState.filters.size > 1 && ( + + Remove column + + )} + +
+ + +
+ ); + })} + + Add column + +
+ + ); +}; diff --git a/website/src/components/views/compareToBaseline/GenericCompareToBaselinePage.astro b/website/src/components/views/compareToBaseline/GenericCompareToBaselinePage.astro index 5095db10d..650f35d58 100644 --- a/website/src/components/views/compareToBaseline/GenericCompareToBaselinePage.astro +++ b/website/src/components/views/compareToBaseline/GenericCompareToBaselinePage.astro @@ -1,56 +1,25 @@ --- -import { GenericCompareToBaselineDataDisplay } from './GenericCompareToBaselineDataDisplay'; +import { GenericCompareToBaselineReactPage } from './GenericCompareToBaselineReactPage'; import { isStaging, getDashboardsConfig } from '../../../config'; -import SingleVariantOrganismPageLayout from '../../../layouts/OrganismPage/SingleVariantOrganismPageLayout.astro'; -import { type OrganismViewKey, type OrganismWithViewKey } from '../../../views/routing'; +import BaseLayout from '../../../layouts/base/BaseLayout.astro'; +import { type OrganismWithViewKey } from '../../../views/routing'; import { ServerSide } from '../../../views/serverSideRouting'; import { compareToBaselineViewKey } from '../../../views/viewKeys'; -import { CompareVariantsToBaselineStateSelector } from '../../pageStateSelectors/CompareVariantsToBaselineStateSelector'; -import { CompareToBaselineSelectorFallback } from '../../pageStateSelectors/FallbackElement'; -import { sanitizeForFilename } from '../compareSideBySide/toDownloadLink'; -type OrganismViewCompareVariant = OrganismWithViewKey; interface Props { - organism: OrganismViewCompareVariant; + organism: OrganismWithViewKey; } const { organism } = Astro.props; -const organismViewKey = `${organism}.${compareToBaselineViewKey}` satisfies OrganismViewKey; -const view = ServerSide.routing.getOrganismView(organismViewKey); -const pageState = view.pageStateHandler.parsePageStateFromUrl(Astro.url); - -const numeratorLapisFilters = view.pageStateHandler.variantFiltersToNamedLapisFilters(pageState); -const noVariantSelected = pageState.variants.size < 1; - -const downloadLinks = noVariantSelected - ? [] - : numeratorLapisFilters.map(({ lapisFilter, displayName }) => ({ - label: `Download accessions of "${displayName}"`, - filter: lapisFilter, - downloadFileBasename: `${organism}_${sanitizeForFilename(displayName)}_accessions`, - })); - -const organismConfig = getDashboardsConfig().dashboards.organisms; +const view = ServerSide.routing.getOrganismView(`${organism}.${compareToBaselineViewKey}`); --- - - + - - -
- -
- + /> + diff --git a/website/src/components/views/compareToBaseline/GenericCompareToBaselineReactPage.tsx b/website/src/components/views/compareToBaseline/GenericCompareToBaselineReactPage.tsx new file mode 100644 index 000000000..b1afb1c0b --- /dev/null +++ b/website/src/components/views/compareToBaseline/GenericCompareToBaselineReactPage.tsx @@ -0,0 +1,63 @@ +import { type FC, useMemo } from 'react'; + +import { GenericCompareToBaselineDataDisplay } from './GenericCompareToBaselineDataDisplay'; +import { type OrganismsConfig } from '../../../config'; +import { SingleVariantOrganismPageLayout } from '../../../layouts/OrganismPage/SingleVariantOrganismPageLayout.tsx'; +import { type OrganismViewKey, type OrganismWithViewKey, Routing } from '../../../views/routing'; +import { compareToBaselineViewKey } from '../../../views/viewKeys'; +import { CompareVariantsToBaselineStateSelector } from '../../pageStateSelectors/CompareVariantsToBaselineStateSelector'; +import { sanitizeForFilename } from '../compareSideBySide/toDownloadLink'; + +export type GenericCompareToBaselineReactPageProps = { + organism: OrganismWithViewKey; + organismsConfig: OrganismsConfig; + isStaging: boolean; +}; + +export const GenericCompareToBaselineReactPage: FC = ({ + organism, + organismsConfig, + isStaging, +}) => { + const organismViewKey = `${organism}.${compareToBaselineViewKey}` satisfies OrganismViewKey; + const view = useMemo( + () => new Routing(organismsConfig).getOrganismView(organismViewKey), + [organismsConfig, organismViewKey], + ); + + const pageState = view.pageStateHandler.parsePageStateFromUrl(new URL(window.location.href)); + + const numeratorLapisFilters = view.pageStateHandler.variantFiltersToNamedLapisFilters(pageState); + const noVariantSelected = pageState.variants.size < 1; + + const downloadLinks = noVariantSelected + ? [] + : numeratorLapisFilters.map(({ lapisFilter, displayName }) => ({ + label: `Download accessions of "${displayName}"`, + filter: lapisFilter, + downloadFileBasename: `${organism}_${sanitizeForFilename(displayName)}_accessions`, + })); + + return ( + + } + dataDisplay={ + + } + /> + ); +}; diff --git a/website/src/components/views/compareVariants/GenericCompareVariantsPage.astro b/website/src/components/views/compareVariants/GenericCompareVariantsPage.astro index 76727768d..4b5a062e1 100644 --- a/website/src/components/views/compareVariants/GenericCompareVariantsPage.astro +++ b/website/src/components/views/compareVariants/GenericCompareVariantsPage.astro @@ -1,55 +1,25 @@ --- -import { GenericCompareVariantsDataDisplay } from './GenericCompareVariantsDataDisplay'; +import { GenericCompareVariantsReactPage } from './GenericCompareVariantsReactPage'; import { isStaging, getDashboardsConfig } from '../../../config'; -import SingleVariantOrganismPageLayout from '../../../layouts/OrganismPage/SingleVariantOrganismPageLayout.astro'; -import { type OrganismViewKey, type OrganismWithViewKey } from '../../../views/routing'; +import BaseLayout from '../../../layouts/base/BaseLayout.astro'; +import { type OrganismWithViewKey } from '../../../views/routing'; import { ServerSide } from '../../../views/serverSideRouting'; import { compareVariantsViewKey } from '../../../views/viewKeys'; -import { CompareVariantsPageStateSelector } from '../../pageStateSelectors/CompareVariantsPageStateSelector'; -import { CompareVariantsSelectorFallback } from '../../pageStateSelectors/FallbackElement'; -import { sanitizeForFilename } from '../compareSideBySide/toDownloadLink'; -type OrganismViewCompareVariant = OrganismWithViewKey; interface Props { - organism: OrganismViewCompareVariant; + organism: OrganismWithViewKey; } const { organism } = Astro.props; -const organismViewKey = `${organism}.${compareVariantsViewKey}` satisfies OrganismViewKey; -const view = ServerSide.routing.getOrganismView(organismViewKey); -const pageState = view.pageStateHandler.parsePageStateFromUrl(Astro.url); - -const numeratorLapisFilters = view.pageStateHandler.variantFiltersToNamedLapisFilters(pageState); -const notEnoughVariantsSelected = pageState.variants.size < 2; -const downloadLinks = notEnoughVariantsSelected - ? [] - : numeratorLapisFilters.map(({ lapisFilter, displayName }) => ({ - label: `Download accessions of "${displayName}"`, - filter: lapisFilter, - downloadFileBasename: `${organism}_${sanitizeForFilename(displayName)}_accessions`, - })); - -const organismConfig = getDashboardsConfig().dashboards.organisms; +const view = ServerSide.routing.getOrganismView(`${organism}.${compareVariantsViewKey}`); --- - - + - - -
- -
- + /> + diff --git a/website/src/components/views/compareVariants/GenericCompareVariantsReactPage.tsx b/website/src/components/views/compareVariants/GenericCompareVariantsReactPage.tsx new file mode 100644 index 000000000..d1b970481 --- /dev/null +++ b/website/src/components/views/compareVariants/GenericCompareVariantsReactPage.tsx @@ -0,0 +1,63 @@ +import { type FC, useMemo } from 'react'; + +import { GenericCompareVariantsDataDisplay } from './GenericCompareVariantsDataDisplay'; +import { type OrganismsConfig } from '../../../config'; +import { SingleVariantOrganismPageLayout } from '../../../layouts/OrganismPage/SingleVariantOrganismPageLayout.tsx'; +import { type OrganismViewKey, type OrganismWithViewKey, Routing } from '../../../views/routing'; +import { compareVariantsViewKey } from '../../../views/viewKeys'; +import { CompareVariantsPageStateSelector } from '../../pageStateSelectors/CompareVariantsPageStateSelector'; +import { sanitizeForFilename } from '../compareSideBySide/toDownloadLink'; + +export type GenericCompareVariantsReactPageProps = { + organism: OrganismWithViewKey; + organismsConfig: OrganismsConfig; + isStaging: boolean; +}; + +export const GenericCompareVariantsReactPage: FC = ({ + organism, + organismsConfig, + isStaging, +}) => { + const organismViewKey = `${organism}.${compareVariantsViewKey}` satisfies OrganismViewKey; + const view = useMemo( + () => new Routing(organismsConfig).getOrganismView(organismViewKey), + [organismsConfig, organismViewKey], + ); + + const pageState = view.pageStateHandler.parsePageStateFromUrl(new URL(window.location.href)); + + const numeratorLapisFilters = view.pageStateHandler.variantFiltersToNamedLapisFilters(pageState); + const notEnoughVariantsSelected = pageState.variants.size < 2; + + const downloadLinks = notEnoughVariantsSelected + ? [] + : numeratorLapisFilters.map(({ lapisFilter, displayName }) => ({ + label: `Download accessions of "${displayName}"`, + filter: lapisFilter, + downloadFileBasename: `${organism}_${sanitizeForFilename(displayName)}_accessions`, + })); + + return ( + + } + dataDisplay={ + + } + /> + ); +}; diff --git a/website/src/components/views/sequencingEfforts/GenericSequencingEffortsPage.astro b/website/src/components/views/sequencingEfforts/GenericSequencingEffortsPage.astro index 45418e0a1..b23520e33 100644 --- a/website/src/components/views/sequencingEfforts/GenericSequencingEffortsPage.astro +++ b/website/src/components/views/sequencingEfforts/GenericSequencingEffortsPage.astro @@ -1,56 +1,25 @@ --- -import { GenericSequencingEffortsDataDisplay } from './GenericSequencingEffortsDataDisplay'; +import { GenericSequencingEffortsReactPage } from './GenericSequencingEffortsReactPage'; import { isStaging, getDashboardsConfig } from '../../../config'; -import SingleVariantOrganismPageLayout from '../../../layouts/OrganismPage/SingleVariantOrganismPageLayout.astro'; -import { type OrganismViewKey, type OrganismWithViewKey } from '../../../views/routing'; +import BaseLayout from '../../../layouts/base/BaseLayout.astro'; +import { type OrganismWithViewKey } from '../../../views/routing'; import { ServerSide } from '../../../views/serverSideRouting'; import { sequencingEffortsViewKey } from '../../../views/viewKeys'; -import { SequencingEffortsSelectorFallback } from '../../pageStateSelectors/FallbackElement'; -import { SequencingEffortsPageStateSelector } from '../../pageStateSelectors/SequencingEffortsPageStateSelector'; -type OrganismViewCompareVariant = OrganismWithViewKey; interface Props { - organism: OrganismViewCompareVariant; + organism: OrganismWithViewKey; } const { organism } = Astro.props; -const organismViewKey: OrganismViewKey = `${organism}.${sequencingEffortsViewKey}` satisfies OrganismViewKey; -const view = ServerSide.routing.getOrganismView(organismViewKey); -const pageState = view.pageStateHandler.parsePageStateFromUrl(Astro.url); - -const lapisFilter = view.pageStateHandler.toLapisFilter(pageState); - -const organismConfig = getDashboardsConfig().dashboards.organisms; +const view = ServerSide.routing.getOrganismView(`${organism}.${sequencingEffortsViewKey}`); --- - - + - - - -
- -
- + /> + diff --git a/website/src/components/views/sequencingEfforts/GenericSequencingEffortsReactPage.tsx b/website/src/components/views/sequencingEfforts/GenericSequencingEffortsReactPage.tsx new file mode 100644 index 000000000..8dea17a2e --- /dev/null +++ b/website/src/components/views/sequencingEfforts/GenericSequencingEffortsReactPage.tsx @@ -0,0 +1,61 @@ +import { type FC, useMemo } from 'react'; + +import { GenericSequencingEffortsDataDisplay } from './GenericSequencingEffortsDataDisplay'; +import { type OrganismsConfig } from '../../../config'; +import { SingleVariantOrganismPageLayout } from '../../../layouts/OrganismPage/SingleVariantOrganismPageLayout.tsx'; +import { type OrganismViewKey, type OrganismWithViewKey, Routing } from '../../../views/routing'; +import { sequencingEffortsViewKey } from '../../../views/viewKeys'; +import { SequencingEffortsPageStateSelector } from '../../pageStateSelectors/SequencingEffortsPageStateSelector'; + +export type GenericSequencingEffortsReactPageProps = { + organism: OrganismWithViewKey; + organismsConfig: OrganismsConfig; + isStaging: boolean; +}; + +export const GenericSequencingEffortsReactPage: FC = ({ + organism, + organismsConfig, + isStaging, +}) => { + const organismViewKey = `${organism}.${sequencingEffortsViewKey}` satisfies OrganismViewKey; + const view = useMemo( + () => new Routing(organismsConfig).getOrganismView(organismViewKey), + [organismsConfig, organismViewKey], + ); + + const pageState = view.pageStateHandler.parsePageStateFromUrl(new URL(window.location.href)); + + const lapisFilter = view.pageStateHandler.toLapisFilter(pageState); + + const downloadLinks = [ + { + label: 'Download accessions', + filter: lapisFilter, + downloadFileBasename: `${organism}_sequencing_efforts_accessions`, + }, + ]; + + return ( + + } + dataDisplay={ + + } + /> + ); +}; diff --git a/website/src/components/views/wasap/Wasap.astro b/website/src/components/views/wasap/Wasap.astro index 2a9c7196f..4c24593d2 100644 --- a/website/src/components/views/wasap/Wasap.astro +++ b/website/src/components/views/wasap/Wasap.astro @@ -1,36 +1,18 @@ --- import { WasapPage } from './WasapPage'; -import { defaultBreadcrumbs } from '../../../layouts/Breadcrumbs'; -import DataPageLayout from '../../../layouts/OrganismPage/DataPageLayout.astro'; -import { dataOrigins } from '../../../types/dataOrigins'; -import { - wastewaterBreadcrumb, - wastewaterOrganismConfigs, - type WastewaterOrganismName, -} from '../../../types/wastewaterConfig'; +import BaseLayout from '../../../layouts/base/BaseLayout.astro'; +import { wastewaterOrganismConfigs, type WastewaterOrganismName } from '../../../types/wastewaterConfig'; type Props = { wastewaterOrganism: WastewaterOrganismName; }; const { wastewaterOrganism } = Astro.props; -const { name, path: href, lapisBaseUrl } = wastewaterOrganismConfigs[wastewaterOrganism]; +const { name } = wastewaterOrganismConfigs[wastewaterOrganism]; const url = Astro.url; --- - + - + diff --git a/website/src/components/views/wasap/WasapPage.tsx b/website/src/components/views/wasap/WasapPage.tsx index 70cc2d2f5..5067ec857 100644 --- a/website/src/components/views/wasap/WasapPage.tsx +++ b/website/src/components/views/wasap/WasapPage.tsx @@ -13,7 +13,14 @@ import { } from './wasapPageConfig'; import { getDateRange } from '../../../lapis/getDateRange'; import { getTotalCount } from '../../../lapis/getTotalCount'; -import { wastewaterOrganismConfigs, type WastewaterOrganismName } from '../../../types/wastewaterConfig'; +import { defaultBreadcrumbs } from '../../../layouts/Breadcrumbs.tsx'; +import { DataPageLayout } from '../../../layouts/OrganismPage/DataPageLayout.tsx'; +import { dataOrigins } from '../../../types/dataOrigins.ts'; +import { + wastewaterBreadcrumb, + wastewaterOrganismConfigs, + type WastewaterOrganismName, +} from '../../../types/wastewaterConfig'; import { Loading } from '../../../util/Loading'; import { WasapPageStateHandler } from '../../../views/pageStateHandlers/WasapPageStateHandler'; import { GsMutationsOverTime } from '../../genspectrum/GsMutationsOverTime'; @@ -64,56 +71,69 @@ export const WasapPageInner: FC = ({ wastewaterOrganism, current const memoizedLinkTemplate = useMemo(() => JSON.stringify(config.linkTemplate), [config.linkTemplate]); return ( - -
-
- -
- {isError ? ( - There was an error fetching the mutations to display. - ) : isPending ? ( - - ) : ( -
- {displayMutations?.length === 0 ? ( - - ) : ( - - )} - {analysis.mode === 'variant' && config.variantAnalysisModeEnabled && ( - - )} - + +
+
+
- )} -
- + {isError ? ( + There was an error fetching the mutations to display. + ) : isPending ? ( + + ) : ( +
+ {displayMutations?.length === 0 ? ( + + ) : ( + + )} + {analysis.mode === 'variant' && config.variantAnalysisModeEnabled && ( + + )} + +
+ )} +
+ + ); }; diff --git a/website/src/lapis/getLastUpdatedDate.spec.ts b/website/src/lapis/getLastUpdatedDate.spec.ts index 410ee68a8..4dea079e4 100644 --- a/website/src/lapis/getLastUpdatedDate.spec.ts +++ b/website/src/lapis/getLastUpdatedDate.spec.ts @@ -28,7 +28,7 @@ describe('getLastUpdatedDate', () => { const result = await getLastUpdatedDate(DUMMY_LAPIS_URL); - expect(result).toBeUndefined(); + expect(result).toBeNull(); }); test('should handle non-numeric data versions gracefully', async () => { @@ -36,6 +36,6 @@ describe('getLastUpdatedDate', () => { const result = await getLastUpdatedDate(DUMMY_LAPIS_URL); - expect(result).toBeUndefined(); + expect(result).toBeNull(); }); }); diff --git a/website/src/lapis/getLastUpdatedDate.ts b/website/src/lapis/getLastUpdatedDate.ts index 4fcdac581..013724881 100644 --- a/website/src/lapis/getLastUpdatedDate.ts +++ b/website/src/lapis/getLastUpdatedDate.ts @@ -2,14 +2,14 @@ import axios from 'axios'; import dayjs from 'dayjs'; import { z } from 'zod'; -import { getInstanceLogger } from '../logger.ts'; +import { getClientLogger } from '../clientLogger.ts'; const lapisInfoSchema = z.object({ dataVersion: z.string(), }); export type LapisInfo = z.infer; -const logger = getInstanceLogger('getLastUpdatedDate'); +const logger = getClientLogger('getLastUpdatedDate'); export async function getLastUpdatedDate(lapisUrl: string) { try { @@ -20,7 +20,7 @@ export async function getLastUpdatedDate(lapisUrl: string) { const timestamp = Number(parsedLapisInfo.data.dataVersion); if (isNaN(timestamp)) { logger.error(`Got invalid timestamp from lapis info: '${parsedLapisInfo.data.dataVersion}'`); - return undefined; + return null; } return dayjs.unix(timestamp).locale('de').calendar(null, { sameElse: '[on] YYYY-MM-DD' }); } @@ -28,9 +28,9 @@ export async function getLastUpdatedDate(lapisUrl: string) { logger.error( `Failed to parse lapis info: ${JSON.stringify(parsedLapisInfo)} (was ${JSON.stringify(response.data)})`, ); - return undefined; + return null; } catch (error) { logger.error(`Failed to fetch lapis info: ${JSON.stringify(error)}`); - return undefined; + return null; } } diff --git a/website/src/layouts/OrganismPage/AccessionsDownloadButton.astro b/website/src/layouts/OrganismPage/AccessionsDownloadButton.astro deleted file mode 100644 index 3457d3132..000000000 --- a/website/src/layouts/OrganismPage/AccessionsDownloadButton.astro +++ /dev/null @@ -1,53 +0,0 @@ ---- -import type { LapisFilter } from '@genspectrum/dashboard-components/util'; - -import { assembleDownloadUrl } from './assembleDownloadUrl'; -import { Modal } from '../../styles/containers/Modal'; -import { ModalContent } from '../../styles/containers/ModalContent'; -import { ModalHeader } from '../../styles/containers/ModalHeader'; - -type DownloadLink = { - label: string; - filter: LapisFilter; - downloadFileBasename: string; -}; - -interface Props { - accessionDownloadFields: string[]; - downloadLinks: DownloadLink[]; - lapisUrl: string; -} - -const { accessionDownloadFields, downloadLinks, lapisUrl } = Astro.props; - -const modalId = 'accessionDownloadModal'; ---- - - - - - -

You can download a list of accessions that are used for the visualizations on this page:

-
- { - downloadLinks - .map(({ label, filter, downloadFileBasename }) => ({ - label, - url: assembleDownloadUrl(accessionDownloadFields, filter, downloadFileBasename, lapisUrl), - })) - .map(({ label, url }) => ( - - - {label} - - )) - } -
-
- -
- - diff --git a/website/src/layouts/OrganismPage/AccessionsDownloadButton.tsx b/website/src/layouts/OrganismPage/AccessionsDownloadButton.tsx new file mode 100644 index 000000000..4bb1fd7a3 --- /dev/null +++ b/website/src/layouts/OrganismPage/AccessionsDownloadButton.tsx @@ -0,0 +1,63 @@ +import type { LapisFilter } from '@genspectrum/dashboard-components/util'; +import type { FC } from 'react'; + +import { assembleDownloadUrl } from './assembleDownloadUrl'; +import { Modal, useModalRef } from '../../styles/containers/Modal'; +import { ModalContent } from '../../styles/containers/ModalContent'; +import { ModalHeader } from '../../styles/containers/ModalHeader'; + +export type DownloadLink = { + label: string; + filter: LapisFilter; + downloadFileBasename: string; +}; + +export type AccessionsDownloadButtonProps = { + accessionDownloadFields: string[]; + downloadLinks: DownloadLink[]; + lapisUrl: string; +}; + +export const AccessionsDownloadButton: FC = ({ + accessionDownloadFields, + downloadLinks, + lapisUrl, +}) => { + const modalRef = useModalRef(); + + return ( + <> + + + + +

You can download a list of accessions that are used for the visualizations on this page:

+
+ {downloadLinks + .map(({ label, filter, downloadFileBasename }) => ({ + label, + url: assembleDownloadUrl( + accessionDownloadFields, + filter, + downloadFileBasename, + lapisUrl, + ), + })) + .map(({ label, url }) => ( + + + {label} + + ))} +
+
+ +
+ + + + ); +}; diff --git a/website/src/layouts/OrganismPage/DataPageLayout.astro b/website/src/layouts/OrganismPage/DataPageLayout.astro deleted file mode 100644 index fbd92a1cf..000000000 --- a/website/src/layouts/OrganismPage/DataPageLayout.astro +++ /dev/null @@ -1,48 +0,0 @@ ---- -import type { ComponentProps } from 'astro/types'; - -import LapisUnreachableWrapperClient from '../../components/LapisUnreachableWrapperClient'; -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'; - -interface Props { - title: string; - breadcrumbs: BreadcrumbElement[]; - dataOrigins: DataOrigin[]; - lapisUrl: string; - downloadLinks?: ComponentProps['downloadLinks']; - accessionDownloadFields?: string[]; -} - -const { title, breadcrumbs, dataOrigins, lapisUrl, downloadLinks = [], accessionDownloadFields = [] } = Astro.props; ---- - - -
-
- -
-
- - - -
-
- { - downloadLinks.length > 0 && ( - - ) - } - - -
-
- diff --git a/website/src/layouts/OrganismPage/DataPageLayout.tsx b/website/src/layouts/OrganismPage/DataPageLayout.tsx new file mode 100644 index 000000000..969d87802 --- /dev/null +++ b/website/src/layouts/OrganismPage/DataPageLayout.tsx @@ -0,0 +1,50 @@ +import type { FC, PropsWithChildren } from 'react'; + +import { LapisUnreachableWrapperClient } from '../../components/LapisUnreachableWrapperClient.tsx'; +import type { DataOrigin } from '../../types/dataOrigins.ts'; +import { type BreadcrumbElement, Breadcrumbs } from '../Breadcrumbs.tsx'; +import { AccessionsDownloadButton, type DownloadLink } from './AccessionsDownloadButton.tsx'; +import { LastUpdatedInfo } from './LastUpdatedInfo.tsx'; +import { withQueryProvider } from '../../components/subscriptions/backendApi/withQueryProvider.tsx'; +import { DataInfo } from '../base/footer/DataInfo.tsx'; + +export type DataPageLayoutProps = PropsWithChildren<{ + breadcrumbs: BreadcrumbElement[]; + dataOrigins: DataOrigin[]; + lapisUrl: string; + downloadLinks?: DownloadLink[]; + accessionDownloadFields?: string[]; +}>; + +export const DataPageLayoutInner: FC = ({ + breadcrumbs, + dataOrigins, + lapisUrl, + downloadLinks = [], + accessionDownloadFields = [], + children, +}) => { + return ( +
+
+ +
+
+ {children} +
+
+ {downloadLinks.length > 0 && ( + + )} + + +
+
+ ); +}; + +export const DataPageLayout = withQueryProvider(DataPageLayoutInner); diff --git a/website/src/layouts/OrganismPage/LastUpdatedInfo.astro b/website/src/layouts/OrganismPage/LastUpdatedInfo.astro deleted file mode 100644 index 1d29acab1..000000000 --- a/website/src/layouts/OrganismPage/LastUpdatedInfo.astro +++ /dev/null @@ -1,13 +0,0 @@ ---- -import { getLastUpdatedDate } from '../../lapis/getLastUpdatedDate'; - -interface Props { - lapisUrl: string; -} - -const { lapisUrl } = Astro.props; - -const lastUpdatedDate = await getLastUpdatedDate(lapisUrl); ---- - -Data last updated: {lastUpdatedDate ?? 'unknown'} diff --git a/website/src/layouts/OrganismPage/LastUpdatedInfo.tsx b/website/src/layouts/OrganismPage/LastUpdatedInfo.tsx new file mode 100644 index 000000000..67eeeae5e --- /dev/null +++ b/website/src/layouts/OrganismPage/LastUpdatedInfo.tsx @@ -0,0 +1,18 @@ +import { useQuery } from '@tanstack/react-query'; +import type { FC } from 'react'; + +import { getLastUpdatedDate } from '../../lapis/getLastUpdatedDate'; + +interface LastUpdatedInfoProps { + lapisUrl: string; +} + +export const LastUpdatedInfo: FC = ({ lapisUrl }) => { + const { data: lastUpdatedDate } = useQuery({ + queryKey: ['lastUpdatedDate', lapisUrl], + queryFn: () => getLastUpdatedDate(lapisUrl), + throwOnError: true, + }); + + return Data last updated: {lastUpdatedDate ?? 'unknown'}; +}; diff --git a/website/src/layouts/OrganismPage/OrganismViewPageLayout.astro b/website/src/layouts/OrganismPage/OrganismViewPageLayout.astro deleted file mode 100644 index 11d51ab7b..000000000 --- a/website/src/layouts/OrganismPage/OrganismViewPageLayout.astro +++ /dev/null @@ -1,33 +0,0 @@ ---- -import type { ComponentProps } from 'astro/types'; - -import AccessionsDownloadButton from './AccessionsDownloadButton.astro'; -import DataPageLayout from './DataPageLayout.astro'; -import { getLapisUrl } from '../../config'; -import type { OrganismConstants } from '../../views/OrganismConstants'; -import { type View } from '../../views/View'; -import type { PageStateHandler } from '../../views/pageStateHandlers/PageStateHandler'; - -interface Props { - view: View>; - downloadLinks: ComponentProps['downloadLinks']; -} - -const { view, downloadLinks } = Astro.props; ---- - - - - - - diff --git a/website/src/layouts/OrganismPage/OrganismViewPageLayout.tsx b/website/src/layouts/OrganismPage/OrganismViewPageLayout.tsx new file mode 100644 index 000000000..d14a6f850 --- /dev/null +++ b/website/src/layouts/OrganismPage/OrganismViewPageLayout.tsx @@ -0,0 +1,34 @@ +import type { FC, PropsWithChildren } from 'react'; + +import { type DownloadLink } from './AccessionsDownloadButton.tsx'; +import { DataPageLayout } from './DataPageLayout.tsx'; +import type { OrganismConstants } from '../../views/OrganismConstants'; +import { type View } from '../../views/View'; +import type { PageStateHandler } from '../../views/pageStateHandlers/PageStateHandler'; + +export type OrganismViewPageLayoutProps = PropsWithChildren<{ + view: View>; + downloadLinks: DownloadLink[]; + lapisUrl: string; +}>; + +export const OrganismViewPageLayout: FC = ({ + view, + downloadLinks, + lapisUrl, + children, +}) => { + return ( + + + {children} + + + ); +}; diff --git a/website/src/layouts/OrganismPage/SingleVariantOrganismPageLayout.astro b/website/src/layouts/OrganismPage/SingleVariantOrganismPageLayout.astro deleted file mode 100644 index 514a91a78..000000000 --- a/website/src/layouts/OrganismPage/SingleVariantOrganismPageLayout.astro +++ /dev/null @@ -1,25 +0,0 @@ ---- -import type { ComponentProps } from 'astro/types'; - -import AccessionsDownloadButton from './AccessionsDownloadButton.astro'; -import OrganismViewPageLayout from './OrganismViewPageLayout.astro'; -import type { OrganismConstants } from '../../views/OrganismConstants'; -import type { View } from '../../views/View'; -import { type PageStateHandler } from '../../views/pageStateHandlers/PageStateHandler'; - -interface Props { - view: View>; - downloadLinks: ComponentProps['downloadLinks']; -} - -const { view, downloadLinks } = Astro.props; ---- - - -
-
- -
- -
- diff --git a/website/src/layouts/OrganismPage/SingleVariantOrganismPageLayout.tsx b/website/src/layouts/OrganismPage/SingleVariantOrganismPageLayout.tsx new file mode 100644 index 000000000..ceebf3a44 --- /dev/null +++ b/website/src/layouts/OrganismPage/SingleVariantOrganismPageLayout.tsx @@ -0,0 +1,37 @@ +import type { FC, ReactNode } from 'react'; + +import { type DownloadLink } from './AccessionsDownloadButton.tsx'; +import { OrganismViewPageLayout } from './OrganismViewPageLayout.tsx'; +import type { OrganismsConfig } from '../../config.ts'; +import type { OrganismConstants } from '../../views/OrganismConstants'; +import type { View } from '../../views/View'; +import { type PageStateHandler } from '../../views/pageStateHandlers/PageStateHandler'; + +export type SingleVariantOrganismPageLayoutProps = { + view: View>; + downloadLinks: DownloadLink[]; + organismsConfig: OrganismsConfig; + filters: ReactNode; + dataDisplay: ReactNode; +}; + +export const SingleVariantOrganismPageLayout: FC = ({ + view, + downloadLinks, + organismsConfig, + filters, + dataDisplay, +}) => { + return ( + +
+
{filters}
+ {dataDisplay} +
+ + ); +}; diff --git a/website/src/layouts/base/footer/DataInfo.astro b/website/src/layouts/base/footer/DataInfo.astro deleted file mode 100644 index 93cc13254..000000000 --- a/website/src/layouts/base/footer/DataInfo.astro +++ /dev/null @@ -1,26 +0,0 @@ ---- -import DataOriginLink from './DataOriginLink.astro'; -import { type DataOrigin, dataOriginConfig } from '../../../types/dataOrigins'; - -interface Props { - dataOrigins: DataOrigin[]; -} - -const { dataOrigins } = Astro.props; ---- - -
-
- Enabled by data from: - { - dataOrigins.map((dataOrigin, index) => ( - - {index > 0 && (index === dataOrigins.length - 1 ? ' and ' : ', ')} - - {dataOriginConfig[dataOrigin].name} - - - )) - } -
-
diff --git a/website/src/layouts/base/footer/DataInfo.tsx b/website/src/layouts/base/footer/DataInfo.tsx new file mode 100644 index 000000000..ae7b3bd6b --- /dev/null +++ b/website/src/layouts/base/footer/DataInfo.tsx @@ -0,0 +1,38 @@ +import { type FC, type PropsWithChildren } from 'react'; + +import { externalLinkIconCss } from '../../../components/iconCss.ts'; +import { type DataOrigin, dataOriginConfig } from '../../../types/dataOrigins'; + +export type DataInfoProps = { + dataOrigins: DataOrigin[]; +}; + +export const DataInfo: FC = ({ dataOrigins }) => { + return ( +
+
+ Enabled by data from: + {dataOrigins.map((dataOrigin, index) => ( + + {index > 0 && (index === dataOrigins.length - 1 ? ' and ' : ', ')} + + {dataOriginConfig[dataOrigin].name} + + + ))} +
+
+ ); +}; + +type DataOriginLinkProps = PropsWithChildren<{ + href: string; +}>; + +const DataOriginLink: FC = ({ href, children }) => { + return ( + + {children} + + ); +}; diff --git a/website/src/layouts/base/footer/DataOriginLink.astro b/website/src/layouts/base/footer/DataOriginLink.astro deleted file mode 100644 index 3e0700e55..000000000 --- a/website/src/layouts/base/footer/DataOriginLink.astro +++ /dev/null @@ -1,12 +0,0 @@ ---- -import { externalLinkIconCss } from '../../../components/iconCss'; -interface Props { - href: string; -} - -const { href } = Astro.props; ---- - - - - diff --git a/website/src/pages/covid/single-variant.astro b/website/src/pages/covid/single-variant.astro index 0a56d0eaa..fa95aaefb 100644 --- a/website/src/pages/covid/single-variant.astro +++ b/website/src/pages/covid/single-variant.astro @@ -1,72 +1,16 @@ --- -import { AnalyzeSingleVariantSelectorFallback } from '../../components/pageStateSelectors/FallbackElement'; -import { SelectorHeadline } from '../../components/pageStateSelectors/SelectorHeadline'; -import { SingleVariantPageStateSelector } from '../../components/pageStateSelectors/SingleVariantPageStateSelector'; -import { CollectionsList } from '../../components/views/analyzeSingleVariant/CollectionsList'; -import { CovidSingleVariantDataDisplay } from '../../components/views/analyzeSingleVariant/CovidSingleVariantDataDisplay'; -import { sanitizeForFilename } from '../../components/views/compareSideBySide/toDownloadLink'; +import { CovidSingleVariantReactPage } from '../../components/views/analyzeSingleVariant/CovidSingleVariantReactPage'; import { isStaging, getDashboardsConfig } from '../../config'; -import SingleVariantOrganismPageLayout from '../../layouts/OrganismPage/SingleVariantOrganismPageLayout.astro'; -import { hasOnlyUndefinedValues } from '../../util/hasOnlyUndefinedValues'; -import { toDisplayName } from '../../views/pageStateHandlers/PageStateHandler'; -import { type OrganismViewKey } from '../../views/routing'; +import BaseLayout from '../../layouts/base/BaseLayout.astro'; import { ServerSide } from '../../views/serverSideRouting'; -const organismViewKey: OrganismViewKey = 'covid.singleVariantView'; -const view = ServerSide.routing.getOrganismView(organismViewKey); -const pageState = view.pageStateHandler.parsePageStateFromUrl(Astro.url); - -const variantFilter = view.pageStateHandler.toLapisFilter(pageState); - -const noVariantSelected = hasOnlyUndefinedValues(pageState.variantFilter); - -const displayName = toDisplayName(pageState.variantFilter); -const downloadLinks = noVariantSelected - ? [ - { - label: 'Download all accessions', - filter: variantFilter, - downloadFileBasename: `${view.organismConstants.organism}_accessions`, - }, - ] - : [ - { - label: `Download accessions of ${displayName}`, - filter: variantFilter, - downloadFileBasename: `${view.organismConstants.organism}_${sanitizeForFilename(displayName)}_accessions`, - }, - ]; -const organismConfig = getDashboardsConfig().dashboards.organisms; +const view = ServerSide.routing.getOrganismView('covid.singleVariantView'); --- - -
- - - -
-
- Collections - -
-
- -
- -
- + + + diff --git a/website/src/pages/index.astro b/website/src/pages/index.astro index be85c87ee..1f93fad8f 100644 --- a/website/src/pages/index.astro +++ b/website/src/pages/index.astro @@ -2,7 +2,7 @@ import Link from '../components/Link.astro'; import MainMenu from '../components/MainMenu.astro'; import BaseLayout from '../layouts/base/BaseLayout.astro'; -import DataInfo from '../layouts/base/footer/DataInfo.astro'; +import { DataInfo } from '../layouts/base/footer/DataInfo.tsx'; import { BrandName } from '../layouts/base/header/Brand'; import { getPathogenMegaMenuSections } from '../layouts/base/header/getPathogenMegaMenuSections'; import { dataOrigins } from '../types/dataOrigins'; diff --git a/website/src/pages/swiss-wastewater/flu.astro b/website/src/pages/swiss-wastewater/flu.astro index 9395dd487..119324242 100644 --- a/website/src/pages/swiss-wastewater/flu.astro +++ b/website/src/pages/swiss-wastewater/flu.astro @@ -4,7 +4,8 @@ import type { SequenceType } from '@genspectrum/dashboard-components/util'; import InfluenzaWastewaterInfo from '../../components/InfluenzaWastewaterInfo.astro'; import GsWastewaterMutationsOverTime from '../../components/genspectrum/GsWastewaterMutationsOverTime.astro'; import { defaultBreadcrumbs } from '../../layouts/Breadcrumbs'; -import DataPageLayout from '../../layouts/OrganismPage/DataPageLayout.astro'; +import { DataPageLayout } from '../../layouts/OrganismPage/DataPageLayout.tsx'; +import BaseLayout from '../../layouts/base/BaseLayout.astro'; import { dataOrigins } from '../../types/dataOrigins'; import { getMutationAnnotation, @@ -16,48 +17,49 @@ import { const lapisUrl = `${wastewaterConfig.lapisBaseUrl}/influenza`; --- - + { - name: 'Influenza', - href: wastewaterConfig.pages.influenza.path, - }, - ]} - dataOrigins={[dataOrigins.wise]} - lapisUrl={lapisUrl} -> - { - InfluenzaTypes.map((reference) => { - const mutationAnnotations = getMutationAnnotation(reference); - return ( - -
-

{reference}

- {(['nucleotide', 'amino acid'] satisfies SequenceType[]).map((sequenceType) => ( - - { + const mutationAnnotations = getMutationAnnotation(reference); + return ( + +
+

{reference}

+ {(['nucleotide', 'amino acid'] satisfies SequenceType[]).map((sequenceType) => ( + - - ))} -
- - ); - }) - } - + collapsible={sequenceType === 'nucleotide'} + linkSuffix={reference} + > + + + ))} +
+ + ); + }) + } + + diff --git a/website/src/pages/swiss-wastewater/rsv.astro b/website/src/pages/swiss-wastewater/rsv.astro index b8ca93065..0a37abb92 100644 --- a/website/src/pages/swiss-wastewater/rsv.astro +++ b/website/src/pages/swiss-wastewater/rsv.astro @@ -4,56 +4,58 @@ import type { SequenceType } from '@genspectrum/dashboard-components/util'; import RsvWastewaterInfo from '../../components/RsvWastewaterInfo.astro'; import GsWastewaterMutationsOverTime from '../../components/genspectrum/GsWastewaterMutationsOverTime.astro'; import { defaultBreadcrumbs } from '../../layouts/Breadcrumbs'; -import DataPageLayout from '../../layouts/OrganismPage/DataPageLayout.astro'; +import { DataPageLayout } from '../../layouts/OrganismPage/DataPageLayout.tsx'; +import BaseLayout from '../../layouts/base/BaseLayout.astro'; import { dataOrigins } from '../../types/dataOrigins'; import { wastewaterConfig, RSVTypes, wastewaterBreadcrumb } from '../../types/wastewaterConfig'; const lapisUrl = `${wastewaterConfig.lapisBaseUrl}/rsv`; --- - - -
+ + ( - <> -
-

{reference}

- {(['nucleotide', 'amino acid'] satisfies SequenceType[]).map((sequenceType) => ( - - + +
+ { + RSVTypes.map((reference) => ( + <> +
+

{reference}

+ {(['nucleotide', 'amino acid'] satisfies SequenceType[]).map((sequenceType) => ( + - - ))} -
- - )) - } -
- - + collapsible={sequenceType === 'nucleotide'} + linkSuffix={reference} + > + + + ))} +
+ + )) + } +
+ + + From 5f769b8158d63623901674cd81aed54edf10db83 Mon Sep 17 00:00:00 2001 From: Fabian Engelniederhammer <92720311+fengelniederhammer@users.noreply.github.com> Date: Tue, 13 Jan 2026 08:20:37 +0100 Subject: [PATCH 22/26] ci: lint PR title instead of commits (#989) * lint PR title instead of commits * remove obsolete scripts * also on "edited" * typo * prevent command line injection * prevent command line injection --- .github/workflows/commitlint.yml | 7 +++++-- CONTRIBUTING.md | 4 +++- package.json | 4 ---- 3 files changed, 8 insertions(+), 7 deletions(-) diff --git a/.github/workflows/commitlint.yml b/.github/workflows/commitlint.yml index 54d7437f9..c3579d2a6 100644 --- a/.github/workflows/commitlint.yml +++ b/.github/workflows/commitlint.yml @@ -4,6 +4,7 @@ on: pull_request: types: - opened + - edited - reopened - synchronize - ready_for_review @@ -29,5 +30,7 @@ jobs: - name: Install npm packages run: npm ci - - name: Validate PR commits with commitlint - run: npx commitlint --from ${{ github.event.pull_request.base.sha }} --verbose + - name: Lint PR title + env: + PR_TITLE: ${{ github.event.pull_request.title }} + run: echo "$PR_TITLE" | npx commitlint --verbose \ No newline at end of file diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index c3bbffc9a..bda464925 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -4,7 +4,9 @@ Contributions are very welcome! Just fork the repository, develop in a branch an ## Commit Messages -We follow [conventional commits](https://www.conventionalcommits.org) when writing commit messages. +Commits on the `main` branch should follow [conventional commits](https://www.conventionalcommits.org). +Since we squash-merge pull requests, the PR title should also follow conventional commits +(because it will become the commit message of the squashed commit). The messages themselves should help future developers understand **why** changes were made. ## Code Style diff --git a/package.json b/package.json index 4b7274c65..007e273f1 100644 --- a/package.json +++ b/package.json @@ -8,9 +8,5 @@ "@commitlint/cli": "^19.4.0", "@commitlint/config-conventional": "^19.2.2", "@commitlint/types": "^19.0.3" - }, - "scripts": { - "commitlint:last-commit": "commitlint --from=HEAD~1 --verbose", - "commitlint:merge-base": "commitlint --from=$(git merge-base HEAD main) --verbose" } } From a29532729e982ef3552ce7f7a4f5e8160ef29498 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 13 Jan 2026 08:21:23 +0100 Subject: [PATCH 23/26] chore(website): bump the minorandpatch group in /website with 5 updates (#993) Bumps the minorandpatch group in /website with 5 updates: | Package | From | To | | --- | --- | --- | | [@tanstack/react-query](https://github.com/TanStack/query/tree/HEAD/packages/react-query) | `5.90.15` | `5.90.16` | | [astro](https://github.com/withastro/astro/tree/HEAD/packages/astro) | `5.16.6` | `5.16.9` | | [@typescript-eslint/eslint-plugin](https://github.com/typescript-eslint/typescript-eslint/tree/HEAD/packages/eslint-plugin) | `8.51.0` | `8.53.0` | | [@typescript-eslint/parser](https://github.com/typescript-eslint/typescript-eslint/tree/HEAD/packages/parser) | `8.51.0` | `8.53.0` | | [typescript-eslint](https://github.com/typescript-eslint/typescript-eslint/tree/HEAD/packages/typescript-eslint) | `8.51.0` | `8.53.0` | Updates `@tanstack/react-query` from 5.90.15 to 5.90.16 - [Release notes](https://github.com/TanStack/query/releases) - [Changelog](https://github.com/TanStack/query/blob/main/packages/react-query/CHANGELOG.md) - [Commits](https://github.com/TanStack/query/commits/@tanstack/react-query@5.90.16/packages/react-query) Updates `astro` from 5.16.6 to 5.16.9 - [Release notes](https://github.com/withastro/astro/releases) - [Changelog](https://github.com/withastro/astro/blob/main/packages/astro/CHANGELOG.md) - [Commits](https://github.com/withastro/astro/commits/astro@5.16.9/packages/astro) Updates `@typescript-eslint/eslint-plugin` from 8.51.0 to 8.53.0 - [Release notes](https://github.com/typescript-eslint/typescript-eslint/releases) - [Changelog](https://github.com/typescript-eslint/typescript-eslint/blob/main/packages/eslint-plugin/CHANGELOG.md) - [Commits](https://github.com/typescript-eslint/typescript-eslint/commits/v8.53.0/packages/eslint-plugin) Updates `@typescript-eslint/parser` from 8.51.0 to 8.53.0 - [Release notes](https://github.com/typescript-eslint/typescript-eslint/releases) - [Changelog](https://github.com/typescript-eslint/typescript-eslint/blob/main/packages/parser/CHANGELOG.md) - [Commits](https://github.com/typescript-eslint/typescript-eslint/commits/v8.53.0/packages/parser) Updates `typescript-eslint` from 8.51.0 to 8.53.0 - [Release notes](https://github.com/typescript-eslint/typescript-eslint/releases) - [Changelog](https://github.com/typescript-eslint/typescript-eslint/blob/main/packages/typescript-eslint/CHANGELOG.md) - [Commits](https://github.com/typescript-eslint/typescript-eslint/commits/v8.53.0/packages/typescript-eslint) --- updated-dependencies: - dependency-name: "@tanstack/react-query" dependency-version: 5.90.16 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: minorandpatch - dependency-name: astro dependency-version: 5.16.9 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: minorandpatch - dependency-name: "@typescript-eslint/eslint-plugin" dependency-version: 8.53.0 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: minorandpatch - dependency-name: "@typescript-eslint/parser" dependency-version: 8.53.0 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: minorandpatch - dependency-name: typescript-eslint dependency-version: 8.53.0 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: minorandpatch ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- website/package-lock.json | 863 +++++++------------------------------- website/package.json | 10 +- 2 files changed, 157 insertions(+), 716 deletions(-) diff --git a/website/package-lock.json b/website/package-lock.json index 62b2c6c83..7d73e8fb0 100644 --- a/website/package-lock.json +++ b/website/package-lock.json @@ -12,8 +12,8 @@ "@astrojs/node": "^9.5.1", "@auth/core": "^0.37.4", "@genspectrum/dashboard-components": "^1.12.0", - "@tanstack/react-query": "^5.90.15", - "astro": "^5.16.6", + "@tanstack/react-query": "^5.90.16", + "astro": "^5.16.9", "auth-astro": "^4.2.0", "axios": "^1.13.2", "cookie": "^1.1.1", @@ -48,8 +48,8 @@ "@types/react-dom": "^18.3.1", "@types/react-katex": "^3.0.4", "@types/topojson-specification": "^1.0.5", - "@typescript-eslint/eslint-plugin": "^8.51.0", - "@typescript-eslint/parser": "^8.51.0", + "@typescript-eslint/eslint-plugin": "^8.53.0", + "@typescript-eslint/parser": "^8.53.0", "@vitest/browser": "^3.2.4", "astro-eslint-parser": "^1.2.2", "daisyui": "^5.5.14", @@ -66,7 +66,7 @@ "prettier-plugin-tailwindcss": "^0.7.2", "tailwindcss": "^4.0.9", "typescript": "^5.9.3", - 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"peer": true, "funding": { "url": "https://github.com/sponsors/colinhacks" } }, "node_modules/zod-to-json-schema": { - "version": "3.25.0", - "resolved": "https://registry.npmjs.org/zod-to-json-schema/-/zod-to-json-schema-3.25.0.tgz", - "integrity": "sha512-HvWtU2UG41LALjajJrML6uQejQhNJx+JBO9IflpSja4R03iNWfKXrj6W2h7ljuLyc1nKS+9yDyL/9tD1U/yBnQ==", + "version": "3.25.1", + "resolved": "https://registry.npmjs.org/zod-to-json-schema/-/zod-to-json-schema-3.25.1.tgz", + "integrity": "sha512-pM/SU9d3YAggzi6MtR4h7ruuQlqKtad8e9S0fmxcMi+ueAK5Korys/aWcV9LIIHTVbj01NdzxcnXSN+O74ZIVA==", "license": "ISC", "peerDependencies": { "zod": "^3.25 || ^4" diff --git a/website/package.json b/website/package.json index 15fe68425..1421e1070 100644 --- a/website/package.json +++ b/website/package.json @@ -27,8 +27,8 @@ "@astrojs/node": "^9.5.1", "@auth/core": "^0.37.4", "@genspectrum/dashboard-components": "^1.12.0", - "@tanstack/react-query": "^5.90.15", - "astro": "^5.16.6", + "@tanstack/react-query": "^5.90.16", + "astro": "^5.16.9", "auth-astro": "^4.2.0", "axios": "^1.13.2", "cookie": "^1.1.1", @@ -63,8 +63,8 @@ "@types/react-dom": "^18.3.1", "@types/react-katex": "^3.0.4", "@types/topojson-specification": "^1.0.5", - "@typescript-eslint/eslint-plugin": "^8.51.0", - "@typescript-eslint/parser": "^8.51.0", + "@typescript-eslint/eslint-plugin": "^8.53.0", + "@typescript-eslint/parser": "^8.53.0", "@vitest/browser": "^3.2.4", "astro-eslint-parser": "^1.2.2", "daisyui": "^5.5.14", @@ -81,7 +81,7 @@ "prettier-plugin-tailwindcss": "^0.7.2", "tailwindcss": "^4.0.9", "typescript": "^5.9.3", - "typescript-eslint": "^8.51.0", + "typescript-eslint": "^8.53.0", "vitest": "^3.2.4", "vitest-browser-react": "^1.0.1", "zod": "^3.25.74" From d87f1520673ece0d5a54674229633cfe05f9d152 Mon Sep 17 00:00:00 2001 From: Felix Hennig Date: Tue, 13 Jan 2026 08:44:24 +0000 Subject: [PATCH 24/26] feat(website): connect real RSV-A backend (#991) --- website/src/types/wastewaterConfig.ts | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/website/src/types/wastewaterConfig.ts b/website/src/types/wastewaterConfig.ts index 1c95f9cbd..1cbc8f9b4 100644 --- a/website/src/types/wastewaterConfig.ts +++ b/website/src/types/wastewaterConfig.ts @@ -28,7 +28,7 @@ export const wastewaterOrganismConfigs: Record Date: Wed, 14 Jan 2026 09:41:53 +0100 Subject: [PATCH 25/26] feat(website): don't reload the whole page when applying the filters (#985) * 984 wip * 984 wip * 984 wip * 984 wip * 984 fix test * 984 fix test * 984 fix lints * 984 rename function * 984 fix map * 984 set type button * 984 fix state update * 984 docstring --- .../genspectrum/GsSequencesByLocation.tsx | 2 + .../ApplyFilterButton.browser.spec.tsx | 77 ++++++++++++------- .../pageStateSelectors/ApplyFilterButton.tsx | 12 ++- .../CompareSideBySidePageStateSelector.tsx | 43 ++++++----- .../CompareVariantsPageStateSelector.tsx | 42 +++++----- ...CompareVariantsToBaselineStateSelector.tsx | 46 +++++------ .../SequencingEffortsPageStateSelector.tsx | 39 +++++----- ...eVariantPageStateSelector.browser.spec.tsx | 43 +++++++---- .../SingleVariantPageStateSelector.tsx | 39 +++++----- .../wasap/WasapPageStateSelector.tsx | 10 ++- .../analyzeSingleVariant/CollectionsList.tsx | 61 ++++++++------- .../CovidSingleVariantDataDisplay.tsx | 21 ++--- .../CovidSingleVariantReactPage.tsx | 18 ++--- ...GenericAnalyseSingleVariantDataDisplay.tsx | 18 ++--- .../GenericAnalyseSingleVariantReactPage.tsx | 15 ++-- .../analyzeSingleVariant/QuickstartLinks.tsx | 23 +++--- .../GenericCompareSideBySideDataDisplay.tsx | 22 ++---- .../GenericCompareSideBySideReactPage.tsx | 12 +-- .../GenericCompareToBaselineDataDisplay.tsx | 22 ++---- .../GenericCompareToBaselineReactPage.tsx | 17 ++-- .../GenericCompareVariantsDataDisplay.tsx | 21 ++--- .../GenericCompareVariantsReactPage.tsx | 17 ++-- .../GenericSequencingEffortsReactPage.tsx | 9 ++- website/src/components/views/usePageState.ts | 34 ++++++++ .../src/components/views/wasap/Wasap.astro | 4 +- .../src/components/views/wasap/WasapPage.tsx | 14 ++-- website/src/views/OrganismConstants.ts | 1 + .../CompareSideBySidePageStateHandler.spec.ts | 1 + .../CompareToBaselinePageStateHandler.spec.ts | 1 + .../CompareVariantsPageStateHandler.spec.ts | 1 + .../SingleVariantPageStateHandler.spec.ts | 1 + 31 files changed, 367 insertions(+), 319 deletions(-) create mode 100644 website/src/components/views/usePageState.ts diff --git a/website/src/components/genspectrum/GsSequencesByLocation.tsx b/website/src/components/genspectrum/GsSequencesByLocation.tsx index 54c51e378..9848e7bed 100644 --- a/website/src/components/genspectrum/GsSequencesByLocation.tsx +++ b/website/src/components/genspectrum/GsSequencesByLocation.tsx @@ -28,6 +28,7 @@ export const GsSequencesByLocation: FC = ({ {mapData === undefined ? ( = ({ /> ) : ( { const handler = new DummyPageStateHandler(); - it('should render enabled link for short URL', () => { + it('should render enabled link for short URL', async () => { const shortState: DummyPageState = { data: 'short' }; - const { getByRole, container } = render( - , + const { result: state } = renderHook(() => useState({ data: 'initial' })); + + const { getByRole } = render( + , ); - const link = getByRole('button'); - expect(link.element()).toBeInTheDocument(); - expect(link.element()).toHaveAttribute('href', '/test?data=short'); - expect(container.textContent).not.toMatch(urlTooLongMessage); + await clickApply(getByRole); + + expect(state.current[0].data).toEqual('short'); }); - it('should render disabled span and error message for long URL', () => { + it('should render disabled span and error message for long URL', async () => { const longData = 'x'.repeat(2000); const longState: DummyPageState = { data: longData }; + const { result: state } = renderHook(() => useState({ data: 'initial' })); + const { getByRole, container } = render( - , + , ); - const button = getByRole('button'); - expect(button.element()).not.toHaveAttribute('href'); expect(container.textContent).toMatch(urlTooLongMessage); + expect(getByRole('button', { name: 'Apply filters' }).element()).not.toHaveAttribute('onClick'); + + await clickApply(getByRole); + expect(state.current[0].data).toEqual('initial'); }); - it('should update when state changes from short to long', () => { + it('should update when state changes from short to long', async () => { const shortState: DummyPageState = { data: 'short' }; + const { result: state } = renderHook(() => useState({ data: 'initial' })); + const { getByRole, container, rerender } = render( - , + , ); - const button = getByRole('button'); - expect(button.element()).toHaveAttribute('href', '/test?data=short'); + await clickApply(getByRole); + expect(state.current[0].data).toEqual('short'); expect(container.textContent).not.toMatch(urlTooLongMessage); const longData = 'x'.repeat(2000); const longState: DummyPageState = { data: longData }; - rerender(); + rerender( + , + ); - const updatedButton = getByRole('button'); - expect(updatedButton.element()).not.toHaveAttribute('href'); expect(container.textContent).toMatch(urlTooLongMessage); + expect(getByRole('button', { name: 'Apply filters' }).element()).not.toHaveAttribute('onClick'); + + await clickApply(getByRole); + expect(state.current[0].data).toEqual('short'); }); - it('should update when state changes from long to short', () => { + it('should update when state changes from long to short', async () => { const longData = 'x'.repeat(2000); const longState: DummyPageState = { data: longData }; + const { result: state } = renderHook(() => useState({ data: 'initial' })); + const { getByRole, container, rerender } = render( - , + , ); - const button = getByRole('button'); - expect(button.element()).not.toHaveAttribute('href'); + expect(getByRole('button', { name: 'Apply filters' }).element()).not.toHaveAttribute('onClick'); expect(container.textContent).toMatch(urlTooLongMessage); + await clickApply(getByRole); + expect(state.current[0].data).toEqual('initial'); const shortState: DummyPageState = { data: 'short' }; - rerender(); + rerender( + , + ); - const updatedButton = getByRole('button'); - expect(updatedButton.element()).toHaveAttribute('href', '/test?data=short'); expect(container.textContent).not.toMatch(urlTooLongMessage); + await clickApply(getByRole); + expect(state.current[0].data).toEqual('short'); }); }); + +async function clickApply(getByRole: RenderResult['getByRole']) { + await act(async () => { + await getByRole('button', { name: 'Apply filters' }).click(); + }); +} diff --git a/website/src/components/pageStateSelectors/ApplyFilterButton.tsx b/website/src/components/pageStateSelectors/ApplyFilterButton.tsx index d01b61b8f..d3d7b5736 100644 --- a/website/src/components/pageStateSelectors/ApplyFilterButton.tsx +++ b/website/src/components/pageStateSelectors/ApplyFilterButton.tsx @@ -1,3 +1,5 @@ +import type { Dispatch, SetStateAction } from 'react'; + import type { WithClassName } from '../../types/WithClassName.ts'; import type { PageStateHandler } from '../../views/pageStateHandlers/PageStateHandler.ts'; @@ -8,15 +10,21 @@ const MAX_URL_LENGTH = 2000; export function ApplyFilterButton({ pageStateHandler, newPageState, + setPageState, className = '', }: WithClassName<{ pageStateHandler: PageStateHandler; newPageState: PageState; + setPageState: Dispatch>; }>) { const url = pageStateHandler.toUrl(newPageState); const fullUrl = `${window.location.origin}${url}`; const urlTooLong = fullUrl.length > MAX_URL_LENGTH; + const applyFilters = () => { + setPageState(newPageState); + }; + return urlTooLong ? ( <> @@ -30,8 +38,8 @@ export function ApplyFilterButton({
) : ( - + ); } diff --git a/website/src/components/pageStateSelectors/CompareSideBySidePageStateSelector.tsx b/website/src/components/pageStateSelectors/CompareSideBySidePageStateSelector.tsx index a71cfc05e..014046f0e 100644 --- a/website/src/components/pageStateSelectors/CompareSideBySidePageStateSelector.tsx +++ b/website/src/components/pageStateSelectors/CompareSideBySidePageStateSelector.tsx @@ -1,37 +1,38 @@ -import { useMemo, useState } from 'react'; +import { type Dispatch, type SetStateAction, useEffect, useMemo, useState } from 'react'; import { ApplyFilterButton } from './ApplyFilterButton.tsx'; import { BaselineSelector } from './BaselineSelector.tsx'; import { SelectorHeadline } from './SelectorHeadline.tsx'; import { makeVariantFilterConfig, VariantSelector } from './VariantSelector.tsx'; -import type { OrganismsConfig } from '../../config.ts'; import { Inset } from '../../styles/Inset.tsx'; +import { BaseView } from '../../views/BaseView.ts'; +import type { OrganismConstants } from '../../views/OrganismConstants.ts'; import type { CompareSideBySideData } from '../../views/View.ts'; -import { type OrganismViewKey, Routing } from '../../views/routing.ts'; -import type { compareSideBySideViewKey } from '../../views/viewKeys.ts'; +import { CompareSideBySideStateHandler } from '../../views/pageStateHandlers/CompareSideBySidePageStateHandler.ts'; export function CompareSideBySidePageStateSelector({ + view, filterId, - initialPageState, - organismViewKey, - organismsConfig, + pageState, + setPageState, enableAdvancedQueryFilter, }: { + view: BaseView; filterId: number; - initialPageState: CompareSideBySideData; - organismViewKey: OrganismViewKey & `${string}.${typeof compareSideBySideViewKey}`; - organismsConfig: OrganismsConfig; + pageState: CompareSideBySideData; + setPageState: Dispatch>; enableAdvancedQueryFilter: boolean; }) { - const view = useMemo(() => new Routing(organismsConfig), [organismsConfig]).getOrganismView(organismViewKey); + const [draftPageState, setDraftPageState] = useState(pageState); + useEffect(() => setDraftPageState(pageState), [pageState]); + const variantFilterConfig = useMemo( () => makeVariantFilterConfig(view.organismConstants), [view.organismConstants], ); - const [pageState, setPageState] = useState(initialPageState); const { filterOfCurrentId, currentLapisFilter } = useMemo(() => { - const filterOfCurrentId = pageState.filters.get(filterId) ?? { + const filterOfCurrentId = draftPageState.filters.get(filterId) ?? { datasetFilter: { locationFilters: {}, dateFilters: {}, @@ -47,7 +48,7 @@ export function CompareSideBySidePageStateSelector({ filterOfCurrentId.variantFilter, ), }; - }, [pageState, filterId, view.pageStateHandler]); + }, [draftPageState, filterId, view.pageStateHandler]); return (
@@ -60,8 +61,8 @@ export function CompareSideBySidePageStateSelector({ lapisFilter={currentLapisFilter} datasetFilter={filterOfCurrentId.datasetFilter} setDatasetFilter={(newDatasetFilter) => { - setPageState((previousState) => { - const updatedFilters = new Map(initialPageState.filters); + setDraftPageState((previousState) => { + const updatedFilters = new Map(previousState.filters); updatedFilters.set(filterId, { ...filterOfCurrentId, datasetFilter: newDatasetFilter, @@ -78,8 +79,8 @@ export function CompareSideBySidePageStateSelector({ { - setPageState((previousState) => { - const updatedFilters = new Map(initialPageState.filters); + setDraftPageState((previousState) => { + const updatedFilters = new Map(previousState.filters); updatedFilters.set(filterId, { ...filterOfCurrentId, variantFilter: newVariantFilter, @@ -96,7 +97,11 @@ export function CompareSideBySidePageStateSelector({
- +
); diff --git a/website/src/components/pageStateSelectors/CompareVariantsPageStateSelector.tsx b/website/src/components/pageStateSelectors/CompareVariantsPageStateSelector.tsx index cbfd106aa..0d03db9c8 100644 --- a/website/src/components/pageStateSelectors/CompareVariantsPageStateSelector.tsx +++ b/website/src/components/pageStateSelectors/CompareVariantsPageStateSelector.tsx @@ -1,39 +1,38 @@ -import { useMemo, useState } from 'react'; +import { type Dispatch, type SetStateAction, useEffect, useMemo, useState } from 'react'; import { ApplyFilterButton } from './ApplyFilterButton.tsx'; import { BaselineSelector } from './BaselineSelector.tsx'; import { SelectorHeadline } from './SelectorHeadline.tsx'; import { makeVariantFilterConfig } from './VariantSelector.tsx'; import { VariantsSelector } from './VariantsSelector.tsx'; -import { type OrganismsConfig } from '../../config.ts'; import { Inset } from '../../styles/Inset.tsx'; +import { GenericCompareVariantsView } from '../../views/BaseView.ts'; +import type { OrganismConstants } from '../../views/OrganismConstants.ts'; import type { CompareVariantsData, Id, VariantFilter } from '../../views/View.ts'; -import { type OrganismViewKey, Routing } from '../../views/routing.ts'; -import type { compareVariantsViewKey } from '../../views/viewKeys.ts'; export function CompareVariantsPageStateSelector({ - organismViewKey, - organismsConfig, - initialPageState, + view, + pageState, + setPageState, enableAdvancedQueryFilter, }: { - organismViewKey: OrganismViewKey & `${string}.${typeof compareVariantsViewKey}`; - organismsConfig: OrganismsConfig; - initialPageState: CompareVariantsData; + view: GenericCompareVariantsView; + pageState: CompareVariantsData; + setPageState: Dispatch>; enableAdvancedQueryFilter: boolean; }) { - const view = useMemo(() => new Routing(organismsConfig), [organismsConfig]).getOrganismView(organismViewKey); - const [pageState, setPageState] = useState(initialPageState); + const [draftPageState, setDraftPageState] = useState(pageState); + useEffect(() => setDraftPageState(pageState), [pageState]); const variantFilterConfigs = useMemo(() => { return new Map( - pageState.variants.entries().map(([id]) => [id, makeVariantFilterConfig(view.organismConstants)]), + draftPageState.variants.entries().map(([id]) => [id, makeVariantFilterConfig(view.organismConstants)]), ); - }, [pageState.variants, view.organismConstants]); + }, [draftPageState.variants, view.organismConstants]); const currentLapisFilter = useMemo(() => { - return view.pageStateHandler.datasetFilterToLapisFilter(pageState.datasetFilter); - }, [pageState, view.pageStateHandler]); + return view.pageStateHandler.datasetFilterToLapisFilter(draftPageState.datasetFilter); + }, [draftPageState, view.pageStateHandler]); return (
@@ -43,9 +42,9 @@ export function CompareVariantsPageStateSelector({ { - setPageState((previousState) => ({ + setDraftPageState((previousState) => ({ ...previousState, datasetFilter: newDatasetFilter, })); @@ -58,10 +57,10 @@ export function CompareVariantsPageStateSelector({ Variant Filters ) => { - setPageState((previousState) => ({ + setDraftPageState((previousState) => ({ ...previousState, variants: newVariantFilters, })); @@ -75,7 +74,8 @@ export function CompareVariantsPageStateSelector({
diff --git a/website/src/components/pageStateSelectors/CompareVariantsToBaselineStateSelector.tsx b/website/src/components/pageStateSelectors/CompareVariantsToBaselineStateSelector.tsx index 5aa4cb498..d57cb6bc5 100644 --- a/website/src/components/pageStateSelectors/CompareVariantsToBaselineStateSelector.tsx +++ b/website/src/components/pageStateSelectors/CompareVariantsToBaselineStateSelector.tsx @@ -1,29 +1,28 @@ -import { useMemo, useState } from 'react'; +import { type Dispatch, type SetStateAction, useEffect, useMemo, useState } from 'react'; import { ApplyFilterButton } from './ApplyFilterButton.tsx'; import { BaselineSelector } from './BaselineSelector.tsx'; import { SelectorHeadline } from './SelectorHeadline.tsx'; import { makeVariantFilterConfig, VariantSelector } from './VariantSelector.tsx'; import { VariantsSelector } from './VariantsSelector.tsx'; -import { type OrganismsConfig } from '../../config.ts'; import { Inset } from '../../styles/Inset.tsx'; +import { GenericCompareToBaselineView } from '../../views/BaseView.ts'; +import type { OrganismConstants } from '../../views/OrganismConstants.ts'; import type { CompareToBaselineData, Id, VariantFilter } from '../../views/View.ts'; -import { type OrganismViewKey, Routing } from '../../views/routing.ts'; -import { type compareToBaselineViewKey } from '../../views/viewKeys.ts'; export function CompareVariantsToBaselineStateSelector({ - organismViewKey, - organismsConfig, - initialPageState, + view, + pageState, + setPageState, enableAdvancedQueryFilter, }: { - organismViewKey: OrganismViewKey & `${string}.${typeof compareToBaselineViewKey}`; - organismsConfig: OrganismsConfig; - initialPageState: CompareToBaselineData; + view: GenericCompareToBaselineView; + pageState: CompareToBaselineData; + setPageState: Dispatch>; enableAdvancedQueryFilter: boolean; }) { - const view = useMemo(() => new Routing(organismsConfig), [organismsConfig]).getOrganismView(organismViewKey); - const [pageState, setPageState] = useState(initialPageState); + const [draftPageState, setDraftPageState] = useState(pageState); + useEffect(() => setDraftPageState(pageState), [pageState]); const variantFilterConfig = useMemo( () => makeVariantFilterConfig(view.organismConstants), @@ -31,12 +30,12 @@ export function CompareVariantsToBaselineStateSelector({ ); const variantFilterConfigs = useMemo(() => { - return new Map(pageState.variants.entries().map(([id]) => [id, { ...variantFilterConfig }])); - }, [pageState.variants, variantFilterConfig]); + return new Map(draftPageState.variants.entries().map(([id]) => [id, { ...variantFilterConfig }])); + }, [draftPageState.variants, variantFilterConfig]); const currentLapisFilter = useMemo(() => { - return view.pageStateHandler.baselineFilterToLapisFilter(pageState); - }, [pageState, view.pageStateHandler]); + return view.pageStateHandler.baselineFilterToLapisFilter(draftPageState); + }, [draftPageState, view.pageStateHandler]); return (
@@ -47,9 +46,9 @@ export function CompareVariantsToBaselineStateSelector({ { - setPageState((previousState) => ({ + setDraftPageState((previousState) => ({ ...previousState, datasetFilter: newDatasetFilter, })); @@ -64,13 +63,13 @@ export function CompareVariantsToBaselineStateSelector({ { - setPageState((previousState) => ({ + setDraftPageState((previousState) => ({ ...previousState, baselineFilter: newVariantFilter, })); }} variantFilterConfig={variantFilterConfig} - variantFilter={pageState.baselineFilter} + variantFilter={draftPageState.baselineFilter} lapisFilter={currentLapisFilter} enableAdvancedQueryFilter={enableAdvancedQueryFilter} /> @@ -81,10 +80,10 @@ export function CompareVariantsToBaselineStateSelector({ Variant Filters ) => { - setPageState((previousState) => ({ + setDraftPageState((previousState) => ({ ...previousState, variants: newVariantFilters, })); @@ -98,7 +97,8 @@ export function CompareVariantsToBaselineStateSelector({
diff --git a/website/src/components/pageStateSelectors/SequencingEffortsPageStateSelector.tsx b/website/src/components/pageStateSelectors/SequencingEffortsPageStateSelector.tsx index ee58b8bca..e095837a5 100644 --- a/website/src/components/pageStateSelectors/SequencingEffortsPageStateSelector.tsx +++ b/website/src/components/pageStateSelectors/SequencingEffortsPageStateSelector.tsx @@ -1,33 +1,31 @@ -import { useMemo, useState } from 'react'; +import { type Dispatch, type SetStateAction, useEffect, useMemo, useState } from 'react'; import { ApplyFilterButton } from './ApplyFilterButton.tsx'; import { BaselineSelector } from './BaselineSelector.tsx'; import { LineageFilterInput } from './LineageFilterInput.tsx'; import { SelectorHeadline } from './SelectorHeadline.tsx'; -import { type OrganismsConfig } from '../../config.ts'; import { Inset } from '../../styles/Inset.tsx'; +import { GenericSequencingEffortsView } from '../../views/BaseView.ts'; +import type { OrganismConstants } from '../../views/OrganismConstants.ts'; import type { DatasetAndVariantData } from '../../views/View.ts'; -import { type OrganismViewKey, Routing } from '../../views/routing.ts'; -import type { sequencingEffortsViewKey } from '../../views/viewKeys.ts'; export function SequencingEffortsPageStateSelector({ - organismViewKey, - organismsConfig, - initialPageState, + view, + pageState, + setPageState, enableAdvancedQueryFilter, }: { - organismViewKey: OrganismViewKey & `${string}.${typeof sequencingEffortsViewKey}`; - organismsConfig: OrganismsConfig; - initialPageState: DatasetAndVariantData; + view: GenericSequencingEffortsView; + pageState: DatasetAndVariantData; + setPageState: Dispatch>; enableAdvancedQueryFilter: boolean; }) { - const view = useMemo(() => new Routing(organismsConfig), [organismsConfig]).getOrganismView(organismViewKey); - - const [pageState, setPageState] = useState(initialPageState); + const [draftPageState, setDraftPageState] = useState(pageState); + useEffect(() => setDraftPageState(pageState), [pageState]); const currentLapisFilter = useMemo(() => { - return view.pageStateHandler.toLapisFilter(pageState); - }, [pageState, view.pageStateHandler]); + return view.pageStateHandler.toLapisFilter(draftPageState); + }, [draftPageState, view.pageStateHandler]); return (
@@ -37,9 +35,9 @@ export function SequencingEffortsPageStateSelector({ { - setPageState((previousState) => ({ + setDraftPageState((previousState) => ({ ...previousState, datasetFilter: newDatasetFilter, })); @@ -50,7 +48,7 @@ export function SequencingEffortsPageStateSelector({ { - setPageState((previousState) => ({ + setDraftPageState((previousState) => ({ ...previousState, variantFilter: { lineages: { @@ -62,7 +60,7 @@ export function SequencingEffortsPageStateSelector({ }} key={lineageFilterConfig.lapisField} lapisFilter={currentLapisFilter} - value={pageState.variantFilter.lineages?.[lineageFilterConfig.lapisField]} + value={draftPageState.variantFilter.lineages?.[lineageFilterConfig.lapisField]} /> ))} @@ -71,7 +69,8 @@ export function SequencingEffortsPageStateSelector({
diff --git a/website/src/components/pageStateSelectors/SingleVariantPageStateSelector.browser.spec.tsx b/website/src/components/pageStateSelectors/SingleVariantPageStateSelector.browser.spec.tsx index b3e4d6b0f..ad9f50fa8 100644 --- a/website/src/components/pageStateSelectors/SingleVariantPageStateSelector.browser.spec.tsx +++ b/website/src/components/pageStateSelectors/SingleVariantPageStateSelector.browser.spec.tsx @@ -1,40 +1,51 @@ +import { act } from '@testing-library/react'; +import { useState } from 'react'; import { describe, expect } from 'vitest'; -import { render } from 'vitest-browser-react'; +import { render, renderHook } from 'vitest-browser-react'; import { SingleVariantPageStateSelector } from './SingleVariantPageStateSelector.tsx'; import { DUMMY_LAPIS_URL, testOrganismsConfig } from '../../../routeMocker.ts'; import { it } from '../../../test-extend'; +import type { CovidVariantData } from '../../views/covid.ts'; +import { Routing } from '../../views/routing.ts'; describe('SingleVariantPageStateSelector', () => { - it('should remember the covid collection id', ({ routeMockers }) => { + it('should remember the covid collection id', async ({ routeMockers }) => { routeMockers.lapis.mockPostAggregated({}, { data: [] }); routeMockers.lapis.mockReferenceGenome({ nucleotideSequences: [{ name: 'main', sequence: 'ATGC' }], genes: [], }); + routeMockers.lapis.mockLineageDefinition('nextcladePangoLineage', {}); - const initialPageState = { - datasetFilter: { - locationFilters: {}, - dateFilters: {}, - textFilters: {}, - numberFilters: {}, - }, - variantFilter: {}, - collectionId: 5, - }; + const { result } = renderHook(() => + useState({ + datasetFilter: { + locationFilters: {}, + dateFilters: {}, + textFilters: {}, + numberFilters: {}, + }, + variantFilter: {}, + collectionId: 5, + }), + ); const { getByRole } = render( , ); - expect(getByRole('button').element()).toHaveAttribute('href', expect.stringContaining('collectionId=5')); + await act(async () => { + await getByRole('button', { name: 'Apply filters' }).click(); + }); + + expect(result.current[0].collectionId).equals(5); }); }); diff --git a/website/src/components/pageStateSelectors/SingleVariantPageStateSelector.tsx b/website/src/components/pageStateSelectors/SingleVariantPageStateSelector.tsx index d9a75c966..cc40f5e0a 100644 --- a/website/src/components/pageStateSelectors/SingleVariantPageStateSelector.tsx +++ b/website/src/components/pageStateSelectors/SingleVariantPageStateSelector.tsx @@ -1,38 +1,38 @@ -import { useMemo, useState } from 'react'; +import { type Dispatch, type SetStateAction, useEffect, useMemo, useState } from 'react'; import { ApplyFilterButton } from './ApplyFilterButton.tsx'; import { BaselineSelector } from './BaselineSelector.tsx'; import { SelectorHeadline } from './SelectorHeadline.tsx'; import { makeVariantFilterConfig, VariantSelector } from './VariantSelector.tsx'; -import { type OrganismsConfig } from '../../config.ts'; import { Inset } from '../../styles/Inset.tsx'; +import type { GenericSingleVariantView } from '../../views/BaseView.ts'; +import type { OrganismConstants } from '../../views/OrganismConstants.ts'; import { type DatasetAndVariantData } from '../../views/View.ts'; -import { type OrganismViewKey, Routing } from '../../views/routing.ts'; -import type { singleVariantViewKey } from '../../views/viewKeys.ts'; export function SingleVariantPageStateSelector({ - organismViewKey, - organismsConfig, - initialPageState, + view, + pageState, + setPageState, enableAdvancedQueryFilter, }: { - organismViewKey: OrganismViewKey & `${string}.${typeof singleVariantViewKey}`; - organismsConfig: OrganismsConfig; - initialPageState: DatasetAndVariantData; + view: GenericSingleVariantView; + pageState: DatasetAndVariantData; + setPageState: Dispatch>; enableAdvancedQueryFilter: boolean; }) { - const view = useMemo(() => new Routing(organismsConfig), [organismsConfig]).getOrganismView(organismViewKey); const variantFilterConfig = useMemo( () => makeVariantFilterConfig(view.organismConstants), [view.organismConstants], ); - const [pageState, setPageState] = useState(initialPageState); + + const [draftPageState, setDraftPageState] = useState(pageState); + useEffect(() => setDraftPageState(pageState), [pageState]); const baselineFilterConfigs = view.organismConstants.baselineFilterConfigs; const currentLapisFilter = useMemo(() => { - return view.pageStateHandler.toLapisFilter(pageState); - }, [pageState, view.pageStateHandler]); + return view.pageStateHandler.toLapisFilter(draftPageState); + }, [draftPageState, view.pageStateHandler]); return (
@@ -42,9 +42,9 @@ export function SingleVariantPageStateSelector({ { - setPageState((previousState) => ({ + setDraftPageState((previousState) => ({ ...previousState, datasetFilter: newDatasetFilter, })); @@ -59,13 +59,13 @@ export function SingleVariantPageStateSelector({ { - setPageState((previousState) => ({ + setDraftPageState((previousState) => ({ ...previousState, variantFilter: newVariantFilter, })); }} variantFilterConfig={variantFilterConfig} - variantFilter={pageState.variantFilter} + variantFilter={draftPageState.variantFilter} lapisFilter={currentLapisFilter} enableAdvancedQueryFilter={enableAdvancedQueryFilter} /> @@ -76,7 +76,8 @@ export function SingleVariantPageStateSelector({
diff --git a/website/src/components/pageStateSelectors/wasap/WasapPageStateSelector.tsx b/website/src/components/pageStateSelectors/wasap/WasapPageStateSelector.tsx index 811c21333..62d18f6de 100644 --- a/website/src/components/pageStateSelectors/wasap/WasapPageStateSelector.tsx +++ b/website/src/components/pageStateSelectors/wasap/WasapPageStateSelector.tsx @@ -1,5 +1,5 @@ import { useQuery } from '@tanstack/react-query'; -import { useState } from 'react'; +import { type Dispatch, type SetStateAction, useState } from 'react'; import { ApplyFilterButton } from '../ApplyFilterButton'; import { DynamicDateFilter } from '../DynamicDateFilter'; @@ -34,11 +34,13 @@ export function WasapPageStateSelector({ pageStateHandler, initialBaseFilterState, initialAnalysisFilterState, + setPageState, }: { config: WasapPageConfig; pageStateHandler: PageStateHandler; initialBaseFilterState: WasapBaseFilter; initialAnalysisFilterState: WasapAnalysisFilter; + setPageState: Dispatch>; }) { const [baseFilterState, setBaseFilterState] = useState(initialBaseFilterState); @@ -201,7 +203,11 @@ export function WasapPageStateSelector({ } })()} - + ); } diff --git a/website/src/components/views/analyzeSingleVariant/CollectionsList.tsx b/website/src/components/views/analyzeSingleVariant/CollectionsList.tsx index 0af04924c..d20b9b051 100644 --- a/website/src/components/views/analyzeSingleVariant/CollectionsList.tsx +++ b/website/src/components/views/analyzeSingleVariant/CollectionsList.tsx @@ -1,15 +1,12 @@ import { useQuery } from '@tanstack/react-query'; -import { useMemo, useState } from 'react'; +import { type Dispatch, type SetStateAction, useState } from 'react'; import { z } from 'zod'; import { getClientLogger } from '../../../clientLogger.ts'; -import type { OrganismsConfig } from '../../../config.ts'; import { type CovidVariantData } from '../../../views/covid.ts'; -import { Routing } from '../../../views/routing.ts'; import { useErrorToast } from '../../ErrorReportInstruction.tsx'; -import { withQueryProvider } from '../../subscriptions/backendApi/withQueryProvider.tsx'; -export const collectionVariantClassName = 'border bg-white px-4 py-2 hover:bg-cyan border-gray-200'; +export const collectionVariantClassName = 'border bg-white px-4 py-2 hover:bg-cyan border-gray-200 cursor-pointer'; type CollectionVariant = { name: string; @@ -25,12 +22,11 @@ type Collection = { type CollectionsListProps = { initialCollectionId?: number; - organismsConfig: OrganismsConfig; + pageState: CovidVariantData; + setPageState: Dispatch>; }; -export const CollectionsList = withQueryProvider(CollectionsListInner); - -function CollectionsListInner({ initialCollectionId, organismsConfig }: CollectionsListProps) { +export function CollectionsList({ initialCollectionId, pageState, setPageState }: CollectionsListProps) { const [selectedCollectionId, setSelectedCollectionId] = useState(initialCollectionId ?? 1); const query = useQuery({ @@ -56,7 +52,8 @@ function CollectionsListInner({ initialCollectionId, organismsConfig }: Collecti /> c.id === selectedCollectionId) ?? query.data[0]} - organismsConfig={organismsConfig} + pageState={pageState} + setPageState={setPageState} /> ); @@ -96,10 +93,11 @@ const querySchema = z.object({ type CollectionVariantListProps = { collection: Collection; - organismsConfig: OrganismsConfig; + pageState: CovidVariantData; + setPageState: Dispatch>; }; -function CollectionVariantList({ collection, organismsConfig }: CollectionVariantListProps) { +function CollectionVariantList({ collection, pageState, setPageState }: CollectionVariantListProps) { const variants = collection.variants; return ( @@ -108,8 +106,9 @@ function CollectionVariantList({ collection, organismsConfig }: CollectionVarian ))} @@ -118,32 +117,37 @@ function CollectionVariantList({ collection, organismsConfig }: CollectionVarian type VariantLinkProps = { variant: CollectionVariant; - organismsConfig: OrganismsConfig; collectionId: number; + pageState: CovidVariantData; + setPageState: Dispatch>; }; -function VariantLink({ variant, organismsConfig, collectionId }: VariantLinkProps) { - const variantLink = useVariantLink(organismsConfig, collectionId, variant); +function VariantLink({ variant, collectionId, pageState, setPageState }: VariantLinkProps) { + const newPageState = useVariantLinkPageState(pageState, collectionId, variant); + + const applyFilters = () => { + if (newPageState === undefined) { + return; + } + setPageState(newPageState); + }; return ( - + ); } const logger = getClientLogger('CollectionList'); -function useVariantLink(organismsConfig: OrganismsConfig, collectionId: number, variant: CollectionVariant) { - const routing = useMemo(() => new Routing(organismsConfig), [organismsConfig]); - +function useVariantLinkPageState( + currentPageState: CovidVariantData, + collectionId: number, + variant: CollectionVariant, +): CovidVariantData | undefined { const { showErrorToast } = useErrorToast(logger); - const currentPageState = routing - .getOrganismView('covid.singleVariantView') - .pageStateHandler.parsePageStateFromUrl(new URL(window.location.href)); - let newPageState: CovidVariantData; - const queryParseResult = querySchema.safeParse(JSON.parse(variant.query)); if (!queryParseResult.success) { @@ -158,7 +162,7 @@ function useVariantLink(organismsConfig: OrganismsConfig, collectionId: number, const query = queryParseResult.data; if (query.variantQuery !== undefined) { - newPageState = { + return { ...currentPageState, collectionId: collectionId, variantFilter: { @@ -168,7 +172,7 @@ function useVariantLink(organismsConfig: OrganismsConfig, collectionId: number, }, }; } else { - newPageState = { + return { ...currentPageState, collectionId: collectionId, variantFilter: { @@ -184,5 +188,4 @@ function useVariantLink(organismsConfig: OrganismsConfig, collectionId: number, }, }; } - return routing.getOrganismView('covid.singleVariantView').pageStateHandler.toUrl(newPageState); } diff --git a/website/src/components/views/analyzeSingleVariant/CovidSingleVariantDataDisplay.tsx b/website/src/components/views/analyzeSingleVariant/CovidSingleVariantDataDisplay.tsx index b07241b50..8ee878318 100644 --- a/website/src/components/views/analyzeSingleVariant/CovidSingleVariantDataDisplay.tsx +++ b/website/src/components/views/analyzeSingleVariant/CovidSingleVariantDataDisplay.tsx @@ -1,17 +1,13 @@ import { views } from '@genspectrum/dashboard-components/util'; -import { type FC, useMemo } from 'react'; +import { type Dispatch, type FC, type SetStateAction } from 'react'; import { CollectionsList } from './CollectionsList.tsx'; import { SelectVariant } from './SelectVariant.tsx'; -import type { OrganismsConfig } from '../../../config.ts'; -import type { Organisms } from '../../../types/Organism.ts'; import { chooseGranularityBasedOnDateRange } from '../../../util/chooseGranularityBasedOnDateRange.ts'; import { hasOnlyUndefinedValues } from '../../../util/hasOnlyUndefinedValues.ts'; -import type { CovidVariantData } from '../../../views/covid.ts'; +import { CovidAnalyzeSingleVariantView, type CovidVariantData } from '../../../views/covid.ts'; import { getLocationSubdivision } from '../../../views/locationHelpers.ts'; import { locationFieldsToFilterIdentifier } from '../../../views/pageStateHandlers/locationFilterFromToUrl.ts'; -import { Routing } from '../../../views/routing.ts'; -import type { singleVariantViewKey } from '../../../views/viewKeys.ts'; import { ComponentsGrid } from '../../ComponentsGrid.tsx'; import { GsAggregate } from '../../genspectrum/GsAggregate.tsx'; import { GsMutations } from '../../genspectrum/GsMutations.tsx'; @@ -21,18 +17,16 @@ import { GsRelativeGrowthAdvantage } from '../../genspectrum/GsRelativeGrowthAdv import { GsStatistics } from '../../genspectrum/GsStatistics.tsx'; export type CovidSingleVariantDataDisplayProps = { - organismViewKey: `${typeof Organisms.covid}.${typeof singleVariantViewKey}`; - organismsConfig: OrganismsConfig; + view: CovidAnalyzeSingleVariantView; pageState: CovidVariantData; + setPageState: Dispatch>; }; export const CovidSingleVariantDataDisplay: FC = ({ - organismViewKey, - organismsConfig, + view, pageState, + setPageState, }) => { - const view = useMemo(() => new Routing(organismsConfig), [organismsConfig]).getOrganismView(organismViewKey); - const variantFilter = view.pageStateHandler.toLapisFilter(pageState); const datasetLapisFilter = view.pageStateHandler.toLapisFilterWithoutVariant(pageState); const timeGranularity = chooseGranularityBasedOnDateRange({ @@ -55,7 +49,8 @@ export const CovidSingleVariantDataDisplay: FC diff --git a/website/src/components/views/analyzeSingleVariant/CovidSingleVariantReactPage.tsx b/website/src/components/views/analyzeSingleVariant/CovidSingleVariantReactPage.tsx index 35b12bad5..438ea46b9 100644 --- a/website/src/components/views/analyzeSingleVariant/CovidSingleVariantReactPage.tsx +++ b/website/src/components/views/analyzeSingleVariant/CovidSingleVariantReactPage.tsx @@ -10,6 +10,7 @@ import { type OrganismViewKey, Routing } from '../../../views/routing.ts'; import { SelectorHeadline } from '../../pageStateSelectors/SelectorHeadline.tsx'; import { SingleVariantPageStateSelector } from '../../pageStateSelectors/SingleVariantPageStateSelector.tsx'; import { sanitizeForFilename } from '../compareSideBySide/toDownloadLink.ts'; +import { usePageState } from '../usePageState.ts'; export type CovidSingleVariantReactPageProps = { organismsConfig: OrganismsConfig; @@ -20,7 +21,7 @@ export const CovidSingleVariantReactPage: FC = const organismViewKey: OrganismViewKey = 'covid.singleVariantView'; const view = useMemo(() => new Routing(organismsConfig).getOrganismView(organismViewKey), [organismsConfig]); - const pageState = view.pageStateHandler.parsePageStateFromUrl(new URL(window.location.href)); + const { pageState, setPageState } = usePageState(view.pageStateHandler); const variantFilter = view.pageStateHandler.toLapisFilter(pageState); @@ -51,9 +52,9 @@ export const CovidSingleVariantReactPage: FC = filters={ <>
@@ -61,17 +62,14 @@ export const CovidSingleVariantReactPage: FC = Collections } dataDisplay={ - + } /> ); diff --git a/website/src/components/views/analyzeSingleVariant/GenericAnalyseSingleVariantDataDisplay.tsx b/website/src/components/views/analyzeSingleVariant/GenericAnalyseSingleVariantDataDisplay.tsx index 8dbdf3865..0bd266e27 100644 --- a/website/src/components/views/analyzeSingleVariant/GenericAnalyseSingleVariantDataDisplay.tsx +++ b/website/src/components/views/analyzeSingleVariant/GenericAnalyseSingleVariantDataDisplay.tsx @@ -1,16 +1,15 @@ import { views } from '@genspectrum/dashboard-components/util'; -import { type FC, useMemo } from 'react'; +import { type Dispatch, type FC, type SetStateAction } from 'react'; import { QuickstartLinks } from './QuickstartLinks.tsx'; import { SelectVariant } from './SelectVariant.tsx'; -import type { OrganismsConfig } from '../../../config.ts'; import { Organisms } from '../../../types/Organism.ts'; import { chooseGranularityBasedOnDateRange } from '../../../util/chooseGranularityBasedOnDateRange.ts'; import { hasOnlyUndefinedValues } from '../../../util/hasOnlyUndefinedValues.ts'; import type { DatasetAndVariantData } from '../../../views/View.ts'; import { getLocationSubdivision } from '../../../views/locationHelpers.ts'; import { locationFieldsToFilterIdentifier } from '../../../views/pageStateHandlers/locationFilterFromToUrl.ts'; -import { type OrganismViewKey, Routing, type SingleVariantOrganism } from '../../../views/routing.ts'; +import { type SingleVariantOrganism, type ViewsMap } from '../../../views/routing.ts'; import type { singleVariantViewKey } from '../../../views/viewKeys.ts'; import { ComponentsGrid } from '../../ComponentsGrid.tsx'; import { GsAggregate } from '../../genspectrum/GsAggregate.tsx'; @@ -20,19 +19,16 @@ import { GsPrevalenceOverTime } from '../../genspectrum/GsPrevalenceOverTime.tsx import { GsStatistics } from '../../genspectrum/GsStatistics.tsx'; export type GenericAnalyseSingleVariantDataDisplayProps = { - organismViewKey: OrganismViewKey & - `${Exclude}.${typeof singleVariantViewKey}`; - organismsConfig: OrganismsConfig; + view: ViewsMap[Exclude][typeof singleVariantViewKey]; pageState: DatasetAndVariantData; + setPageState: Dispatch>; }; export const GenericAnalyseSingleVariantDataDisplay: FC = ({ - organismViewKey, - organismsConfig, + view, pageState, + setPageState, }) => { - const view = useMemo(() => new Routing(organismsConfig), [organismsConfig]).getOrganismView(organismViewKey); - const variantLapisFilter = view.pageStateHandler.toLapisFilter(pageState); const datasetLapisFilter = view.pageStateHandler.toLapisFilterWithoutVariant(pageState); const timeGranularity = chooseGranularityBasedOnDateRange({ @@ -52,7 +48,7 @@ export const GenericAnalyseSingleVariantDataDisplay: FC {noVariantSelected && ( - + )} diff --git a/website/src/components/views/analyzeSingleVariant/GenericAnalyseSingleVariantReactPage.tsx b/website/src/components/views/analyzeSingleVariant/GenericAnalyseSingleVariantReactPage.tsx index 3a9c770f8..477e9a5a8 100644 --- a/website/src/components/views/analyzeSingleVariant/GenericAnalyseSingleVariantReactPage.tsx +++ b/website/src/components/views/analyzeSingleVariant/GenericAnalyseSingleVariantReactPage.tsx @@ -10,6 +10,7 @@ import { type OrganismViewKey, type OrganismWithViewKey, Routing } from '../../. import { singleVariantViewKey } from '../../../views/viewKeys'; import { SingleVariantPageStateSelector } from '../../pageStateSelectors/SingleVariantPageStateSelector'; import { sanitizeForFilename } from '../compareSideBySide/toDownloadLink'; +import { usePageState } from '../usePageState.ts'; export type GenericAnalyseSingleVariantReactPageProps = { organism: Exclude, typeof Organisms.covid>; @@ -28,7 +29,7 @@ export const GenericAnalyseSingleVariantReactPage: FC } dataDisplay={ - + } /> ); diff --git a/website/src/components/views/analyzeSingleVariant/QuickstartLinks.tsx b/website/src/components/views/analyzeSingleVariant/QuickstartLinks.tsx index 9745d57d8..86eac39e9 100644 --- a/website/src/components/views/analyzeSingleVariant/QuickstartLinks.tsx +++ b/website/src/components/views/analyzeSingleVariant/QuickstartLinks.tsx @@ -1,8 +1,8 @@ -import type { FC } from 'react'; +import type { Dispatch, FC, SetStateAction } from 'react'; import { collectionVariantClassName } from './CollectionsList'; import { Organisms } from '../../../types/Organism'; -import type { DatasetFilter } from '../../../views/View.ts'; +import type { DatasetAndVariantData, DatasetFilter } from '../../../views/View.ts'; import { toDisplayName } from '../../../views/pageStateHandlers/PageStateHandler'; import type { SingleVariantOrganism, ViewsMap } from '../../../views/routing'; import { singleVariantViewKey } from '../../../views/viewKeys'; @@ -10,9 +10,10 @@ import { singleVariantViewKey } from '../../../views/viewKeys'; export type QuickstartLinksProps = { view: ViewsMap[Exclude][typeof singleVariantViewKey]; datasetFilter: DatasetFilter; + setPageState: Dispatch>; }; -export const QuickstartLinks: FC = ({ view, datasetFilter }) => { +export const QuickstartLinks: FC = ({ view, datasetFilter, setPageState }) => { const variants = view.organismConstants.predefinedVariants; return ( @@ -21,13 +22,17 @@ export const QuickstartLinks: FC = ({ view, datasetFilter
{variants.map((variant) => { - const href = view.pageStateHandler.toUrl({ - datasetFilter: datasetFilter, - variantFilter: variant, - }); + const applyFilters = () => { + setPageState({ + datasetFilter: datasetFilter, + variantFilter: variant, + }); + }; + + const displayName = toDisplayName(variant); return ( - - {toDisplayName(variant)} + + {displayName} ); })} diff --git a/website/src/components/views/compareSideBySide/GenericCompareSideBySideDataDisplay.tsx b/website/src/components/views/compareSideBySide/GenericCompareSideBySideDataDisplay.tsx index 53921b476..76e5da97c 100644 --- a/website/src/components/views/compareSideBySide/GenericCompareSideBySideDataDisplay.tsx +++ b/website/src/components/views/compareSideBySide/GenericCompareSideBySideDataDisplay.tsx @@ -1,36 +1,28 @@ -import { type FC, useMemo } from 'react'; +import { type FC } from 'react'; -import type { OrganismsConfig } from '../../../config.ts'; import { Organisms } from '../../../types/Organism.ts'; import { chooseGranularityBasedOnDateRange } from '../../../util/chooseGranularityBasedOnDateRange.ts'; -import { ComponentHeight } from '../../../views/OrganismConstants.ts'; -import type { DatasetAndVariantData } from '../../../views/View.ts'; +import { BaseView } from '../../../views/BaseView.ts'; +import { ComponentHeight, type OrganismConstants } from '../../../views/OrganismConstants.ts'; +import type { CompareSideBySideData, DatasetAndVariantData } from '../../../views/View.ts'; +import { CompareSideBySideStateHandler } from '../../../views/pageStateHandlers/CompareSideBySidePageStateHandler.ts'; import { toLapisFilterWithoutVariant } from '../../../views/pageStateHandlers/toLapisFilterWithoutVariant.ts'; -import { type OrganismWithViewKey, Routing } from '../../../views/routing.ts'; -import { compareSideBySideViewKey } from '../../../views/viewKeys.ts'; import { GsAggregate } from '../../genspectrum/GsAggregate.tsx'; import { GsMutations } from '../../genspectrum/GsMutations.tsx'; import { GsPrevalenceOverTime } from '../../genspectrum/GsPrevalenceOverTime.tsx'; import { GsRelativeGrowthAdvantage } from '../../genspectrum/GsRelativeGrowthAdvantage.tsx'; export type GenericCompareSideBySideDataDisplayProps = { - organismViewKey: `${OrganismWithViewKey}.${typeof compareSideBySideViewKey}`; - organismsConfig: OrganismsConfig; + view: BaseView; datasetAndVariantData: DatasetAndVariantData; hideMutationComponents?: boolean; }; export const GenericCompareSideBySideDataDisplay: FC = ({ - organismViewKey, - organismsConfig, + view, datasetAndVariantData, hideMutationComponents, }) => { - const view = useMemo( - () => new Routing(organismsConfig).getOrganismView(organismViewKey), - [organismsConfig, organismViewKey], - ); - const { datasetFilter, variantFilter } = datasetAndVariantData; const datasetLapisFilter = toLapisFilterWithoutVariant(datasetFilter, view.organismConstants.additionalFilters); diff --git a/website/src/components/views/compareSideBySide/GenericCompareSideBySideReactPage.tsx b/website/src/components/views/compareSideBySide/GenericCompareSideBySideReactPage.tsx index 20e72eede..e4f3b5a2c 100644 --- a/website/src/components/views/compareSideBySide/GenericCompareSideBySideReactPage.tsx +++ b/website/src/components/views/compareSideBySide/GenericCompareSideBySideReactPage.tsx @@ -7,6 +7,7 @@ import { OrganismViewPageLayout } from '../../../layouts/OrganismPage/OrganismVi import { type OrganismViewKey, type OrganismWithViewKey, Routing } from '../../../views/routing'; import { compareSideBySideViewKey } from '../../../views/viewKeys'; import { CompareSideBySidePageStateSelector } from '../../pageStateSelectors/CompareSideBySidePageStateSelector'; +import { usePageState } from '../usePageState.ts'; export type GenericCompareSideBySideReactPageProps = { organism: OrganismWithViewKey; @@ -28,7 +29,7 @@ export const GenericCompareSideBySideReactPage: FC )}
diff --git a/website/src/components/views/compareToBaseline/GenericCompareToBaselineDataDisplay.tsx b/website/src/components/views/compareToBaseline/GenericCompareToBaselineDataDisplay.tsx index 39dc1bb01..f2f7163ee 100644 --- a/website/src/components/views/compareToBaseline/GenericCompareToBaselineDataDisplay.tsx +++ b/website/src/components/views/compareToBaseline/GenericCompareToBaselineDataDisplay.tsx @@ -1,31 +1,19 @@ -import { type FC, useMemo } from 'react'; +import { type FC } from 'react'; import { SelectBaseline } from './SelectBaseline.tsx'; -import type { OrganismsConfig } from '../../../config.ts'; import { chooseGranularityBasedOnDateRange } from '../../../util/chooseGranularityBasedOnDateRange.ts'; -import { ComponentHeight } from '../../../views/OrganismConstants.ts'; +import { GenericCompareToBaselineView } from '../../../views/BaseView.ts'; +import { ComponentHeight, type OrganismConstants } from '../../../views/OrganismConstants.ts'; import type { CompareToBaselineData } from '../../../views/View.ts'; -import { type OrganismWithViewKey, Routing } from '../../../views/routing.ts'; -import { compareToBaselineViewKey } from '../../../views/viewKeys.ts'; import { ComponentsGrid } from '../../ComponentsGrid.tsx'; import { GsPrevalenceOverTime } from '../../genspectrum/GsPrevalenceOverTime.tsx'; export type GenericCompareToBaselineDisplayProps = { - organismViewKey: `${OrganismWithViewKey}.${typeof compareToBaselineViewKey}`; - organismsConfig: OrganismsConfig; + view: GenericCompareToBaselineView; pageState: CompareToBaselineData; }; -export const GenericCompareToBaselineDataDisplay: FC = ({ - organismViewKey, - organismsConfig, - pageState, -}) => { - const view = useMemo( - () => new Routing(organismsConfig).getOrganismView(organismViewKey), - [organismsConfig, organismViewKey], - ); - +export const GenericCompareToBaselineDataDisplay: FC = ({ view, pageState }) => { const baselineLapisFilter = view.pageStateHandler.baselineFilterToLapisFilter(pageState); const timeGranularity = chooseGranularityBasedOnDateRange({ earliestDate: new Date(view.organismConstants.earliestDate), diff --git a/website/src/components/views/compareToBaseline/GenericCompareToBaselineReactPage.tsx b/website/src/components/views/compareToBaseline/GenericCompareToBaselineReactPage.tsx index b1afb1c0b..b6b71b463 100644 --- a/website/src/components/views/compareToBaseline/GenericCompareToBaselineReactPage.tsx +++ b/website/src/components/views/compareToBaseline/GenericCompareToBaselineReactPage.tsx @@ -7,6 +7,7 @@ import { type OrganismViewKey, type OrganismWithViewKey, Routing } from '../../. import { compareToBaselineViewKey } from '../../../views/viewKeys'; import { CompareVariantsToBaselineStateSelector } from '../../pageStateSelectors/CompareVariantsToBaselineStateSelector'; import { sanitizeForFilename } from '../compareSideBySide/toDownloadLink'; +import { usePageState } from '../usePageState.ts'; export type GenericCompareToBaselineReactPageProps = { organism: OrganismWithViewKey; @@ -25,7 +26,7 @@ export const GenericCompareToBaselineReactPage: FC - } - dataDisplay={ - } + dataDisplay={} /> ); }; diff --git a/website/src/components/views/compareVariants/GenericCompareVariantsDataDisplay.tsx b/website/src/components/views/compareVariants/GenericCompareVariantsDataDisplay.tsx index 2b57434cd..6610477b3 100644 --- a/website/src/components/views/compareVariants/GenericCompareVariantsDataDisplay.tsx +++ b/website/src/components/views/compareVariants/GenericCompareVariantsDataDisplay.tsx @@ -1,33 +1,22 @@ -import { type FC, useMemo } from 'react'; +import { type FC } from 'react'; import { SelectVariants } from './SelectVariants.tsx'; -import type { OrganismsConfig } from '../../../config.ts'; import { chooseGranularityBasedOnDateRange } from '../../../util/chooseGranularityBasedOnDateRange.ts'; +import { GenericCompareVariantsView } from '../../../views/BaseView.ts'; +import type { OrganismConstants } from '../../../views/OrganismConstants.ts'; import type { CompareVariantsData } from '../../../views/View.ts'; -import { type OrganismWithViewKey, Routing } from '../../../views/routing.ts'; -import { compareVariantsViewKey } from '../../../views/viewKeys.ts'; import { ComponentsGrid } from '../../ComponentsGrid.tsx'; import { GsMutationComparison } from '../../genspectrum/GsMutationComparison.tsx'; import { GsPrevalenceOverTime } from '../../genspectrum/GsPrevalenceOverTime.tsx'; export type GenericCompareVariantsDataDisplayProps = { - organismViewKey: `${OrganismWithViewKey}.${typeof compareVariantsViewKey}`; - organismsConfig: OrganismsConfig; + view: GenericCompareVariantsView; pageState: CompareVariantsData; }; const componentHeight = '540px'; // prevalence over time table with 10 rows -export const GenericCompareVariantsDataDisplay: FC = ({ - organismViewKey, - organismsConfig, - pageState, -}) => { - const view = useMemo( - () => new Routing(organismsConfig).getOrganismView(organismViewKey), - [organismsConfig, organismViewKey], - ); - +export const GenericCompareVariantsDataDisplay: FC = ({ view, pageState }) => { const datasetLapisFilter = view.pageStateHandler.datasetFilterToLapisFilter(pageState.datasetFilter); const timeGranularity = chooseGranularityBasedOnDateRange({ earliestDate: new Date(view.organismConstants.earliestDate), diff --git a/website/src/components/views/compareVariants/GenericCompareVariantsReactPage.tsx b/website/src/components/views/compareVariants/GenericCompareVariantsReactPage.tsx index d1b970481..cffaa97fe 100644 --- a/website/src/components/views/compareVariants/GenericCompareVariantsReactPage.tsx +++ b/website/src/components/views/compareVariants/GenericCompareVariantsReactPage.tsx @@ -7,6 +7,7 @@ import { type OrganismViewKey, type OrganismWithViewKey, Routing } from '../../. import { compareVariantsViewKey } from '../../../views/viewKeys'; import { CompareVariantsPageStateSelector } from '../../pageStateSelectors/CompareVariantsPageStateSelector'; import { sanitizeForFilename } from '../compareSideBySide/toDownloadLink'; +import { usePageState } from '../usePageState.ts'; export type GenericCompareVariantsReactPageProps = { organism: OrganismWithViewKey; @@ -25,7 +26,7 @@ export const GenericCompareVariantsReactPage: FC - } - dataDisplay={ - } + dataDisplay={} /> ); }; diff --git a/website/src/components/views/sequencingEfforts/GenericSequencingEffortsReactPage.tsx b/website/src/components/views/sequencingEfforts/GenericSequencingEffortsReactPage.tsx index 8dea17a2e..865a06470 100644 --- a/website/src/components/views/sequencingEfforts/GenericSequencingEffortsReactPage.tsx +++ b/website/src/components/views/sequencingEfforts/GenericSequencingEffortsReactPage.tsx @@ -6,6 +6,7 @@ import { SingleVariantOrganismPageLayout } from '../../../layouts/OrganismPage/S import { type OrganismViewKey, type OrganismWithViewKey, Routing } from '../../../views/routing'; import { sequencingEffortsViewKey } from '../../../views/viewKeys'; import { SequencingEffortsPageStateSelector } from '../../pageStateSelectors/SequencingEffortsPageStateSelector'; +import { usePageState } from '../usePageState.ts'; export type GenericSequencingEffortsReactPageProps = { organism: OrganismWithViewKey; @@ -24,7 +25,7 @@ export const GenericSequencingEffortsReactPage: FC } diff --git a/website/src/components/views/usePageState.ts b/website/src/components/views/usePageState.ts new file mode 100644 index 000000000..0dafacecc --- /dev/null +++ b/website/src/components/views/usePageState.ts @@ -0,0 +1,34 @@ +import { type Dispatch, type SetStateAction, useCallback, useMemo, useState } from 'react'; + +import type { PageStateHandler } from '../../views/pageStateHandlers/PageStateHandler.ts'; + +/** + * Given a `PageStateHandler`, this hook initially parses the page state from the current URL. + * It returns a `pageState` object and a `setPageState` function. + * When the function is called, + * the new page state is turned into a URL and set as the current URL (added to the page history). + * This way, the URL and current page state are kept in sync. + */ +export function usePageState>(pageStateHandler: StateHandler) { + type PageState = StateHandler extends PageStateHandler ? PS : never; + + const [pageState, setPageStateRaw] = useState( + () => pageStateHandler.parsePageStateFromUrl(new URL(window.location.href)) as PageState, + ); + + const setPageState: Dispatch> = useCallback( + (newPageStateOrUpdater) => { + setPageStateRaw((prevState) => { + const newPageState = + typeof newPageStateOrUpdater === 'function' + ? newPageStateOrUpdater(prevState) + : newPageStateOrUpdater; + window.history.pushState(undefined, '', pageStateHandler.toUrl(newPageState)); + return newPageState; + }); + }, + [pageStateHandler], + ); + + return useMemo(() => ({ pageState, setPageState }), [pageState, setPageState]); +} diff --git a/website/src/components/views/wasap/Wasap.astro b/website/src/components/views/wasap/Wasap.astro index 4c24593d2..4535ed13f 100644 --- a/website/src/components/views/wasap/Wasap.astro +++ b/website/src/components/views/wasap/Wasap.astro @@ -9,10 +9,8 @@ type Props = { const { wastewaterOrganism } = Astro.props; const { name } = wastewaterOrganismConfigs[wastewaterOrganism]; - -const url = Astro.url; --- - + diff --git a/website/src/components/views/wasap/WasapPage.tsx b/website/src/components/views/wasap/WasapPage.tsx index 5067ec857..296b85aed 100644 --- a/website/src/components/views/wasap/WasapPage.tsx +++ b/website/src/components/views/wasap/WasapPage.tsx @@ -26,20 +26,21 @@ import { WasapPageStateHandler } from '../../../views/pageStateHandlers/WasapPag import { GsMutationsOverTime } from '../../genspectrum/GsMutationsOverTime'; import { WasapPageStateSelector } from '../../pageStateSelectors/wasap/WasapPageStateSelector'; import { withQueryProvider } from '../../subscriptions/backendApi/withQueryProvider'; +import { usePageState } from '../usePageState.ts'; export type WasapPageProps = { wastewaterOrganism: WastewaterOrganismName; - currentUrl: URL; }; -export const WasapPageInner: FC = ({ wastewaterOrganism, currentUrl }) => { +export const WasapPageInner: FC = ({ wastewaterOrganism }) => { const config = wastewaterOrganismConfigs[wastewaterOrganism]; // initialize page state from the URL const pageStateHandler = useMemo(() => new WasapPageStateHandler(config), [config]); - const { base, analysis } = useMemo( - () => pageStateHandler.parsePageStateFromUrl(currentUrl), - [pageStateHandler, currentUrl], - ); + + const { + pageState: { base, analysis }, + setPageState, + } = usePageState(pageStateHandler); // fetch which mutations should be analyzed const { data, isPending, isError } = useWasapPageData(config, analysis); @@ -95,6 +96,7 @@ export const WasapPageInner: FC = ({ wastewaterOrganism, current pageStateHandler={pageStateHandler} initialBaseFilterState={base} initialAnalysisFilterState={analysis} + setPageState={setPageState} /> {isError ? ( diff --git a/website/src/views/OrganismConstants.ts b/website/src/views/OrganismConstants.ts index e3c32330c..b6c349517 100644 --- a/website/src/views/OrganismConstants.ts +++ b/website/src/views/OrganismConstants.ts @@ -24,6 +24,7 @@ type AggregatedVisualizations = { export interface OrganismConstants { readonly organism: Organism; + readonly earliestDate: string; readonly dataOrigins: DataOrigin[]; readonly accessionDownloadFields: string[]; readonly mainDateField: string; diff --git a/website/src/views/pageStateHandlers/CompareSideBySidePageStateHandler.spec.ts b/website/src/views/pageStateHandlers/CompareSideBySidePageStateHandler.spec.ts index a369acc58..99e178fb6 100644 --- a/website/src/views/pageStateHandlers/CompareSideBySidePageStateHandler.spec.ts +++ b/website/src/views/pageStateHandlers/CompareSideBySidePageStateHandler.spec.ts @@ -9,6 +9,7 @@ const mockDateRangeOption = { label: 'Last 7 Days', dateFrom: '2024-11-22', date const mockConstants: OrganismConstants = { organism: Organisms.covid, + earliestDate: 'earliestDate', dataOrigins: [], locationFields: ['country', 'region'], mainDateField: 'date', diff --git a/website/src/views/pageStateHandlers/CompareToBaselinePageStateHandler.spec.ts b/website/src/views/pageStateHandlers/CompareToBaselinePageStateHandler.spec.ts index 174923786..29f131f63 100644 --- a/website/src/views/pageStateHandlers/CompareToBaselinePageStateHandler.spec.ts +++ b/website/src/views/pageStateHandlers/CompareToBaselinePageStateHandler.spec.ts @@ -9,6 +9,7 @@ const mockDateRangeOption = { label: 'Last 7 Days', dateFrom: '2024-11-22', date const mockConstants: OrganismConstants = { organism: Organisms.covid, + earliestDate: 'earliestDate', dataOrigins: [], locationFields: ['country', 'region'], mainDateField: 'date', diff --git a/website/src/views/pageStateHandlers/CompareVariantsPageStateHandler.spec.ts b/website/src/views/pageStateHandlers/CompareVariantsPageStateHandler.spec.ts index 5d05f6de0..fbdce1b4f 100644 --- a/website/src/views/pageStateHandlers/CompareVariantsPageStateHandler.spec.ts +++ b/website/src/views/pageStateHandlers/CompareVariantsPageStateHandler.spec.ts @@ -9,6 +9,7 @@ const mockDateRangeOption = { label: 'Last 7 Days', dateFrom: '2024-11-22', date const mockConstants: OrganismConstants = { organism: Organisms.covid, + earliestDate: 'earliestDate', dataOrigins: [], locationFields: ['country', 'region'], mainDateField: 'date', diff --git a/website/src/views/pageStateHandlers/SingleVariantPageStateHandler.spec.ts b/website/src/views/pageStateHandlers/SingleVariantPageStateHandler.spec.ts index cc9f7ce34..785986390 100644 --- a/website/src/views/pageStateHandlers/SingleVariantPageStateHandler.spec.ts +++ b/website/src/views/pageStateHandlers/SingleVariantPageStateHandler.spec.ts @@ -9,6 +9,7 @@ const mockDateRangeOption = { label: 'Last 7 Days', dateFrom: '2024-11-22', date const mockConstants: OrganismConstants = { organism: Organisms.covid, + earliestDate: 'earliestDate', dataOrigins: [], locationFields: ['country', 'region'], mainDateField: 'date', From 33494f03d399ec3cd5439bfbbb136e04d883e4b1 Mon Sep 17 00:00:00 2001 From: Felix Hennig Date: Wed, 14 Jan 2026 12:09:44 +0000 Subject: [PATCH 26/26] fix(tests): increase timeout (#994) --- website/tests/compareSideBySide.spec.ts | 2 ++ 1 file changed, 2 insertions(+) diff --git a/website/tests/compareSideBySide.spec.ts b/website/tests/compareSideBySide.spec.ts index 2ccfa925e..102df74d4 100644 --- a/website/tests/compareSideBySide.spec.ts +++ b/website/tests/compareSideBySide.spec.ts @@ -9,6 +9,8 @@ test.describe('The Compare Side-By-Side page', () => { test(`should show diagrams after selecting a variant in both columns - ${organism}`, async ({ compareSideBySidePage, }) => { + test.setTimeout(60_000); // there is a lot of data to load, so we need the test to run longer + const options = organismOptions[organism]; await compareSideBySidePage.goto(organism);