diff --git a/components/package-lock.json b/components/package-lock.json index a1460e0f..a11f7e54 100644 --- a/components/package-lock.json +++ b/components/package-lock.json @@ -21,6 +21,7 @@ "flatpickr": "^4.6.13", "gridjs": "^6.2.0", "lit": "^3.1.3", + "object-hash": "^3.0.0", "preact": "^10.20.1", "zod": "^3.23.0" }, @@ -40,6 +41,7 @@ "@storybook/web-components": "^8.0.9", "@storybook/web-components-vite": "^8.0.9", "@types/node": "^20.12.7", + "@types/object-hash": "^3.0.6", "@typescript-eslint/eslint-plugin": "^7.14.1", "@typescript-eslint/parser": "^7.14.1", "autoprefixer": "^10.4.19", @@ -6222,6 +6224,18 @@ "undici-types": "~5.26.4" } }, + "node_modules/@types/normalize-package-data": { + "version": "2.4.4", + "resolved": "https://registry.npmjs.org/@types/normalize-package-data/-/normalize-package-data-2.4.4.tgz", + "integrity": "sha512-37i+OaWTh9qeK4LSHPsyRC7NahnGotNuZvjLSgcPzblpHB3rrCJxAOgI5gCdKm7coonsaX1Of0ILiTcnZjbfxA==", + "dev": true + }, + "node_modules/@types/object-hash": { + "version": "3.0.6", + "resolved": "https://registry.npmjs.org/@types/object-hash/-/object-hash-3.0.6.tgz", + "integrity": "sha512-fOBV8C1FIu2ELinoILQ+ApxcUKz4ngq+IWUYrxSGjXzzjUALijilampwkMgEtJ+h2njAW3pi853QpzNVCHB73w==", + "dev": true + }, "node_modules/@types/parse-json": { "version": "4.0.2", "resolved": "https://registry.npmjs.org/@types/parse-json/-/parse-json-4.0.2.tgz", @@ -17335,7 +17349,6 @@ "version": "3.0.0", "resolved": "https://registry.npmjs.org/object-hash/-/object-hash-3.0.0.tgz", "integrity": "sha512-RSn9F68PjH9HqtltsSnqYC1XXoWe9Bju5+213R98cNGttag9q9yAOTzdbsqvIa7aNm5WffBZFpWYr2aWrklWAw==", - "dev": true, "engines": { "node": ">= 6" } diff --git a/components/package.json b/components/package.json index 4de5d7d5..500c7796 100644 --- a/components/package.json +++ b/components/package.json @@ -68,6 +68,7 @@ "flatpickr": "^4.6.13", "gridjs": "^6.2.0", "lit": "^3.1.3", + "object-hash": "^3.0.0", "preact": "^10.20.1", "zod": "^3.23.0" }, @@ -87,6 +88,7 @@ "@storybook/web-components": "^8.0.9", "@storybook/web-components-vite": "^8.0.9", "@types/node": "^20.12.7", + "@types/object-hash": "^3.0.6", "@typescript-eslint/eslint-plugin": "^7.14.1", "@typescript-eslint/parser": "^7.14.1", "autoprefixer": "^10.4.19", diff --git a/components/src/constants.ts b/components/src/constants.ts index b00fe78d..a44a7ead 100644 --- a/components/src/constants.ts +++ b/components/src/constants.ts @@ -1,4 +1,4 @@ -export const LAPIS_URL = 'https://lapis.cov-spectrum.org/open/v2/'; +export const LAPIS_URL = 'https://lapis.cov-spectrum.org/open/v2'; export const AGGREGATED_ENDPOINT = `${LAPIS_URL}/sample/aggregated`; export const NUCLEOTIDE_MUTATIONS_ENDPOINT = `${LAPIS_URL}/sample/nucleotideMutations`; diff --git a/components/src/operator/FillMissingOperator.spec.ts b/components/src/operator/FillMissingOperator.spec.ts index 5cf26020..1e5c0d63 100644 --- a/components/src/operator/FillMissingOperator.spec.ts +++ b/components/src/operator/FillMissingOperator.spec.ts @@ -10,7 +10,9 @@ describe('FillMissingOperator', () => { const query = new FillMissingOperator( child, 'id', - (ids) => [Math.min(...ids), Math.max(...ids)], + (ids) => { + return { min: Math.min(...ids), max: Math.max(...ids) }; + }, (min, max) => { const result = []; for (let i = min; i <= max; i++) { diff --git a/components/src/operator/FillMissingOperator.ts b/components/src/operator/FillMissingOperator.ts index 004fafc7..663f768d 100644 --- a/components/src/operator/FillMissingOperator.ts +++ b/components/src/operator/FillMissingOperator.ts @@ -5,7 +5,9 @@ export class FillMissingOperator implements constructor( private child: Operator, private keyField: KeyToFill, - private getMinMaxFn: (values: Iterable) => [Data[KeyToFill], Data[KeyToFill]] | null, + private getMinMaxFn: ( + values: Iterable, + ) => { min: Data[KeyToFill]; max: Data[KeyToFill] } | null, private getAllRequiredKeysFn: (min: Data[KeyToFill], max: Data[KeyToFill]) => Data[KeyToFill][], private defaultValueFn: (key: Data[KeyToFill]) => Data, ) {} @@ -17,7 +19,7 @@ export class FillMissingOperator implements if (minMax === null) { return childEvaluated; } - const [min, max] = minMax; + const { min, max } = minMax; const requiredKeys = this.getAllRequiredKeysFn(min, max); const content = childEvaluated.content; for (const key of requiredKeys) { diff --git a/components/src/preact/mutationComparison/queryMutationData.ts b/components/src/preact/mutationComparison/queryMutationData.ts index 165bdaf9..e02155cc 100644 --- a/components/src/preact/mutationComparison/queryMutationData.ts +++ b/components/src/preact/mutationComparison/queryMutationData.ts @@ -28,6 +28,17 @@ export function filterMutationData( data: MutationData[], displayedSegments: DisplayedSegment[], displayedMutationTypes: DisplayedMutationType[], +) { + return data.map((mutationEntry) => ({ + displayName: mutationEntry.displayName, + data: filterBySegmentAndMutationType(mutationEntry.data, displayedSegments, displayedMutationTypes), + })); +} + +export function filterBySegmentAndMutationType( + data: SubstitutionOrDeletionEntry[], + displayedSegments: DisplayedSegment[], + displayedMutationTypes: DisplayedMutationType[], ) { const byDisplayedSegments = (mutationEntry: SubstitutionOrDeletionEntry) => { if (mutationEntry.mutation.segment === undefined) { @@ -45,8 +56,5 @@ export function filterMutationData( ); }; - return data.map((mutationEntry) => ({ - displayName: mutationEntry.displayName, - data: mutationEntry.data.filter(byDisplayedSegments).filter(byDisplayedMutationTypes), - })); + return data.filter(byDisplayedSegments).filter(byDisplayedMutationTypes); } diff --git a/components/src/preact/mutationOverTime/__mockData__/aggregated_date.json b/components/src/preact/mutationOverTime/__mockData__/aggregated_date.json new file mode 100644 index 00000000..0cd6f4a2 --- /dev/null +++ b/components/src/preact/mutationOverTime/__mockData__/aggregated_date.json @@ -0,0 +1,642 @@ +{ + "data": [ + { + "count": 122, + "date": "2024-05-13" + }, + { + "count": 48, + "date": "2024-05-12" + }, + { + "count": 1008, + "date": "2024-01-23" + }, + { + "count": 169, + "date": "2024-04-03" + }, + { + "count": 103, + "date": "2024-05-14" + }, + { + "count": 427, + "date": "2024-03-04" + }, + { + "count": 94, + "date": "2024-05-07" + }, + { + "count": 45, + "date": "2024-05-05" + }, + { + "count": 106, + "date": "2024-04-24" + }, + { + "count": 42, + "date": "2024-05-04" + }, + { + "count": 65, + "date": "2024-05-03" + }, + { + "count": 589, + "date": "2024-02-21" + }, + { + "count": 89, + "date": "2024-05-02" + }, + { + "count": 55, + "date": "2024-03-30" + }, + { + "count": 98, + "date": "2024-05-01" + }, + { + "count": 48, + "date": "2024-05-18" + }, + { + "count": 658, + "date": "2024-02-02" + }, + { + "count": 122, + "date": "2024-04-29" + }, + { + "count": 42, + "date": "2024-04-28" + }, + { + "count": 167, + "date": "2024-04-02" + }, + { + "count": 53, + "date": "2024-04-27" + }, + { + "count": 42, + "date": "2024-04-21" + }, + { + "count": 52, + "date": "2024-04-20" + }, + { + "count": 99, + "date": "2024-05-15" + }, + { + "count": 109, + "date": "2024-04-18" + }, + { + "count": 115, + "date": "2024-04-17" + }, + { + "count": 87, + "date": "2024-04-12" + }, + { + "count": 131, + "date": "2024-04-15" + }, + { + "count": 51, + "date": "2024-06-01" + }, + { + "count": 103, + "date": "2024-04-11" + }, + { + "count": 105, + "date": "2024-04-30" + }, + { + "count": 132, + "date": "2024-03-28" + }, + { + "count": 97, + "date": "2024-05-08" + }, + { + "count": 203, + "date": "2024-02-24" + }, + { + "count": 560, + "date": "2024-01-19" + }, + { + "count": 99, + "date": "2024-05-28" + }, + { + "count": 131, + "date": "2024-04-10" + }, + { + "count": 399, + "date": "2024-02-04" + }, + { + "count": 539, + "date": "2024-02-15" + }, + { + "count": 104, + "date": "2024-04-05" + }, + { + "count": 924, + "date": "2024-01-16" + }, + { + "count": 7, + "date": "2024-06-20" + }, + { + "count": 364, + "date": "2024-03-05" + }, + { + "count": 52, + "date": "2024-04-13" + }, + { + "count": 447, + "date": "2024-02-23" + }, + { + "count": 925, + "date": "2024-01-30" + }, + { + "count": 179, + "date": "2024-03-02" + }, + { + "count": 59, + "date": "2024-05-11" + }, + { + "count": 315, + "date": "2024-02-29" + }, + { + "count": 552, + "date": "2024-02-26" + }, + { + "count": 29, + "date": "2024-06-16" + }, + { + "count": 481, + "date": "2024-02-28" + }, + { + "count": 973, + "date": "2024-02-06" + }, + { + "count": 818, + "date": "2024-02-07" + }, + { + "count": 156, + "date": "2024-03-10" + }, + { + "count": 171, + "date": "2024-03-09" + }, + { + "count": 101, + "date": "2024-06-05" + }, + { + "count": 160, + "date": "2024-03-15" + }, + { + "count": 284, + "date": "2024-02-18" + }, + { + "count": 137, + "date": "2024-05-20" + }, + { + "count": 62, + "date": "2024-06-11" + }, + { + "count": 155, + "date": "2024-03-22" + }, + { + "count": 47, + "date": "2024-06-12" + }, + { + "count": 26, + "date": "2024-06-17" + }, + { + "count": 72, + "date": "2024-05-29" + }, + { + "count": 266, + "date": "2024-03-01" + }, + { + "count": 74, + "date": "2024-06-06" + }, + { + "count": 15, + "date": "2024-06-15" + }, + { + "count": 514, + "date": "2024-01-21" + }, + { + "count": 325, + "date": "2024-03-07" + }, + { + "count": 30, + "date": "2024-06-18" + }, + { + "count": 431, + "date": "2024-01-20" + }, + { + "count": 829, + "date": "2024-02-12" + }, + { + "count": 26, + "date": "2024-06-19" + }, + { + "count": 121, + "date": "2024-05-30" + }, + { + "count": 38, + "date": "2024-06-08" + }, + { + "count": 106, + "date": "2024-06-03" + }, + { + "count": 175, + "date": "2024-03-20" + }, + { + "count": 89, + "date": "2024-04-23" + }, + { + "count": 115, + "date": "2024-05-16" + }, + { + "count": 45, + "date": "2024-05-26" + }, + { + "count": 97, + "date": "2024-05-31" + }, + { + "count": 163, + "date": "2024-03-26" + }, + { + "count": 280, + "date": "2024-02-17" + }, + { + "count": 61, + "date": "2024-06-07" + }, + { + "count": 34, + "date": "2024-05-25" + }, + { + "count": 537, + "date": "2024-02-19" + }, + { + "count": 48, + "date": "2024-06-13" + }, + { + "count": 120, + "date": "2024-05-21" + }, + { + "count": 201, + "date": "2024-03-14" + }, + { + "count": 32, + "date": "2024-06-14" + }, + { + "count": 55, + "date": "2024-05-27" + }, + { + "count": 101, + "date": "2024-06-10" + }, + { + "count": 67, + "date": "2024-05-24" + }, + { + "count": 88, + "date": "2024-05-23" + }, + { + "count": 101, + "date": "2024-05-22" + }, + { + "count": 90, + "date": "2024-06-04" + }, + { + "count": 795, + "date": "2024-01-18" + }, + { + "count": 89, + "date": "2024-03-17" + }, + { + "count": 313, + "date": "2024-02-11" + }, + { + "count": 272, + "date": "2024-03-08" + }, + { + "count": 538, + "date": "2024-02-20" + }, + { + "count": 622, + "date": "2024-01-26" + }, + { + "count": 41, + "date": "2024-06-02" + }, + { + "count": 631, + "date": "2024-02-14" + }, + { + "count": 420, + "date": "2024-02-03" + }, + { + "count": 1047, + "date": "2024-01-29" + }, + { + "count": 95, + "date": "2024-04-16" + }, + { + "count": 556, + "date": "2024-02-13" + }, + { + "count": 620, + "date": "2024-02-09" + }, + { + "count": 99, + "date": "2024-04-25" + }, + { + "count": 393, + "date": "2024-01-28" + }, + { + "count": 173, + "date": "2024-03-21" + }, + { + "count": 420, + "date": "2024-01-27" + }, + { + "count": 819, + "date": "2024-01-25" + }, + { + "count": 62, + "date": "2024-05-17" + }, + { + "count": 890, + "date": "2024-01-31" + }, + { + "count": 247, + "date": "2024-02-25" + }, + { + "count": 259, + "date": "2024-03-13" + }, + { + "count": 865, + "date": "2024-01-24" + }, + { + "count": 69, + "date": "2024-05-10" + }, + { + "count": 215, + "date": "2024-03-12" + }, + { + "count": 888, + "date": "2024-01-15" + }, + { + "count": 583, + "date": "2024-02-22" + }, + { + "count": 942, + "date": "2024-02-05" + }, + { + "count": 1095, + "date": "2024-01-22" + }, + { + "count": 82, + "date": "2024-04-26" + }, + { + "count": 795, + "date": "2024-02-01" + }, + { + "count": 39, + "date": "2024-05-19" + }, + { + "count": 375, + "date": "2024-02-10" + }, + { + "count": 86, + "date": "2024-03-16" + }, + { + "count": 209, + "date": "2024-03-18" + }, + { + "count": 955, + "date": "2024-01-17" + }, + { + "count": 150, + "date": "2024-03-19" + }, + { + "count": 90, + "date": "2024-03-23" + }, + { + "count": 78, + "date": "2024-03-24" + }, + { + "count": 189, + "date": "2024-03-25" + }, + { + "count": 79, + "date": "2024-04-19" + }, + { + "count": 152, + "date": "2024-03-03" + }, + { + "count": 184, + "date": "2024-03-27" + }, + { + "count": 517, + "date": "2024-02-27" + }, + { + "count": 694, + "date": "2024-02-08" + }, + { + "count": 108, + "date": "2024-04-22" + }, + { + "count": 94, + "date": "2024-03-29" + }, + { + "count": 399, + "date": "2024-03-06" + }, + { + "count": 47, + "date": "2024-06-09" + }, + { + "count": 63, + "date": "2024-03-31" + }, + { + "count": 51, + "date": "2024-04-14" + }, + { + "count": 440, + "date": "2024-02-16" + }, + { + "count": 162, + "date": "2024-04-01" + }, + { + "count": 132, + "date": "2024-04-09" + }, + { + "count": 148, + "date": "2024-04-04" + }, + { + "count": 96, + "date": "2024-05-09" + }, + { + "count": 108, + "date": "2024-05-06" + }, + { + "count": 83, + "date": "2024-04-06" + }, + { + "count": 72, + "date": "2024-04-07" + }, + { + "count": 271, + "date": "2024-03-11" + }, + { + "count": 152, + "date": "2024-04-08" + } + ], + "info": { + "dataVersion": "1720033519", + "requestId": "55588610-c570-444b-b8ee-f86f3cab90e4", + "requestInfo": "sars_cov-2_nextstrain_open on lapis.cov-spectrum.org at 2024-07-17T15:34:30.664528725", + "reportTo": "Please report to https://github.com/GenSpectrum/LAPIS/issues in case you encounter any unexpected issues. Please include the request ID and the requestInfo in your report." + } +} diff --git a/components/src/preact/mutationOverTime/__mockData__/nucleotideMutations_2024_01.json b/components/src/preact/mutationOverTime/__mockData__/nucleotideMutations_2024_01.json new file mode 100644 index 00000000..4a5e2fbc --- /dev/null +++ b/components/src/preact/mutationOverTime/__mockData__/nucleotideMutations_2024_01.json @@ -0,0 +1,1747 @@ +{ + "data": [ + { + "mutation": "C21T", + "count": 1856, + "proportion": 0.927536231884058, + "sequenceName": null, + "mutationFrom": "C", + "mutationTo": "T", + "position": 21 + }, + { + "mutation": "C44T", + "count": 2330, + "proportion": 0.5814824057898678, + "sequenceName": null, + "mutationFrom": "C", + "mutationTo": "T", + "position": 44 + }, + { + "mutation": "C241T", + "count": 23447, + "proportion": 0.9991903179067587, + "sequenceName": null, + "mutationFrom": "C", + "mutationTo": "T", + "position": 241 + }, + { + "mutation": "T670G", + "count": 24266, + "proportion": 0.9941007783695207, + "sequenceName": null, + "mutationFrom": "T", + "mutationTo": "G", + "position": 670 + }, + { + "mutation": "C774T", + "count": 6257, + "proportion": 0.25756390729839873, + "sequenceName": null, + "mutationFrom": "C", + "mutationTo": "T", + "position": 774 + }, + { + "mutation": "C897A", + "count": 24251, + "proportion": 0.9923479826499714, + "sequenceName": null, + "mutationFrom": "C", + "mutationTo": "A", + "position": 897 + }, + { + "mutation": "C1762A", + "count": 1647, + "proportion": 0.06653470146238992, + "sequenceName": null, + "mutationFrom": "C", + "mutationTo": "A", + "position": 1762 + }, + { + "mutation": "C2790T", + "count": 22917, + "proportion": 0.9999563661750589, + "sequenceName": null, + "mutationFrom": "C", + "mutationTo": "T", + "position": 2790 + }, + { + "mutation": "C3037T", + "count": 24867, + "proportion": 0.9999597876789448, + "sequenceName": null, + "mutationFrom": "C", + "mutationTo": "T", + "position": 3037 + }, + { + "mutation": "G3431T", + "count": 22362, + "proportion": 0.9984818717628148, + "sequenceName": null, + "mutationFrom": "G", + "mutationTo": "T", + "position": 3431 + }, + { + "mutation": "T3565C", + "count": 24401, + "proportion": 0.9968135953266065, + "sequenceName": null, + "mutationFrom": "T", + "mutationTo": "C", + "position": 3565 + }, + { + "mutation": "G4184A", + "count": 24866, + "proportion": 0.999959786061849, + "sequenceName": null, + "mutationFrom": "G", + "mutationTo": "A", + "position": 4184 + }, + { + "mutation": "C4321T", + "count": 24518, + "proportion": 0.9912270062664241, + "sequenceName": null, + "mutationFrom": "C", + "mutationTo": "T", + "position": 4321 + }, + { + "mutation": "A6183G", + "count": 24488, + "proportion": 0.9932668126875963, + "sequenceName": null, + "mutationFrom": "A", + "mutationTo": "G", + "position": 6183 + }, + { + "mutation": "A7842G", + "count": 24819, + "proportion": 0.9985515992757996, + "sequenceName": null, + "mutationFrom": "A", + "mutationTo": "G", + "position": 7842 + }, + { + "mutation": "C8293T", + "count": 24785, + "proportion": 0.9991131535453702, + "sequenceName": null, + "mutationFrom": "C", + "mutationTo": "T", + "position": 8293 + }, + { + "mutation": "G8393A", + "count": 24848, + "proportion": 0.9991154000804182, + "sequenceName": null, + "mutationFrom": "G", + "mutationTo": "A", + "position": 8393 + }, + { + "mutation": "C9344T", + "count": 24858, + "proportion": 0.9999597731203991, + "sequenceName": null, + "mutationFrom": "C", + "mutationTo": "T", + "position": 9344 + }, + { + "mutation": "A9424G", + "count": 24515, + "proportion": 0.9988998451633934, + "sequenceName": null, + "mutationFrom": "A", + "mutationTo": "G", + "position": 9424 + }, + { + "mutation": "C9534T", + "count": 24635, + "proportion": 0.9996347995455284, + "sequenceName": null, + "mutationFrom": "C", + "mutationTo": "T", + "position": 9534 + }, + { + "mutation": "C10029T", + "count": 24344, + "proportion": 0.9999589238036558, + 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Please include the request ID and the requestInfo in your report." + } +} diff --git a/components/src/preact/mutationOverTime/__mockData__/nucleotideMutations_2024_02.json b/components/src/preact/mutationOverTime/__mockData__/nucleotideMutations_2024_02.json new file mode 100644 index 00000000..eb9b5463 --- /dev/null +++ b/components/src/preact/mutationOverTime/__mockData__/nucleotideMutations_2024_02.json @@ -0,0 +1,1774 @@ +{ + "data": [ + { + "mutation": "C21T", + "count": 1009, + "proportion": 0.9474178403755869, + "sequenceName": null, + "mutationFrom": "C", + "mutationTo": "T", + "position": 21 + }, + { + "mutation": "C44T", + "count": 1543, + "proportion": 0.5566378066378066, + "sequenceName": null, + "mutationFrom": "C", + "mutationTo": "T", + "position": 44 + }, + { + "mutation": "C241T", + "count": 14900, + "proportion": 0.997856951513528, + "sequenceName": null, + "mutationFrom": "C", + "mutationTo": "T", + "position": 241 + }, + { + "mutation": "A518-", + "count": 775, + 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Please include the request ID and the requestInfo in your report." + } +} diff --git a/components/src/preact/mutationOverTime/__mockData__/nucleotideMutations_2024_03.json b/components/src/preact/mutationOverTime/__mockData__/nucleotideMutations_2024_03.json new file mode 100644 index 00000000..b81e08d5 --- /dev/null +++ b/components/src/preact/mutationOverTime/__mockData__/nucleotideMutations_2024_03.json @@ -0,0 +1,1819 @@ +{ + "data": [ + { + "mutation": "C21T", + "count": 314, + "proportion": 0.8532608695652174, + "sequenceName": null, + "mutationFrom": "C", + "mutationTo": "T", + "position": 21 + }, + { + "mutation": "C44T", + "count": 530, + "proportion": 0.47790802524797116, + "sequenceName": null, + "mutationFrom": "C", + "mutationTo": "T", + "position": 44 + }, + { + "mutation": "C241T", + "count": 5588, + "proportion": 0.9983919957119886, + "sequenceName": null, + "mutationFrom": "C", + "mutationTo": "T", + "position": 241 + }, + { + "mutation": "G515-", + "count": 285, + 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Please include the request ID and the requestInfo in your report." + } +} diff --git a/components/src/preact/mutationOverTime/__mockData__/nucleotideMutations_2024_04.json b/components/src/preact/mutationOverTime/__mockData__/nucleotideMutations_2024_04.json new file mode 100644 index 00000000..ff14d0f5 --- /dev/null +++ b/components/src/preact/mutationOverTime/__mockData__/nucleotideMutations_2024_04.json @@ -0,0 +1,1864 @@ +{ + "data": [ + { + "mutation": "C21T", + "count": 120, + "proportion": 0.7741935483870968, + "sequenceName": null, + "mutationFrom": "C", + "mutationTo": "T", + "position": 21 + }, + { + "mutation": "C44T", + "count": 292, + "proportion": 0.5367647058823529, + "sequenceName": null, + "mutationFrom": "C", + "mutationTo": "T", + "position": 44 + }, + { + "mutation": "C241T", + "count": 2820, + "proportion": 0.9985835694050992, + "sequenceName": null, + "mutationFrom": "C", + "mutationTo": "T", + "position": 241 + }, + { + "mutation": "G515-", + "count": 157, + 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Please include the request ID and the requestInfo in your report." + } +} diff --git a/components/src/preact/mutationOverTime/__mockData__/nucleotideMutations_2024_06.json b/components/src/preact/mutationOverTime/__mockData__/nucleotideMutations_2024_06.json new file mode 100644 index 00000000..ff14d0f5 --- /dev/null +++ b/components/src/preact/mutationOverTime/__mockData__/nucleotideMutations_2024_06.json @@ -0,0 +1,1864 @@ +{ + "data": [ + { + "mutation": "C21T", + "count": 120, + "proportion": 0.7741935483870968, + "sequenceName": null, + "mutationFrom": "C", + "mutationTo": "T", + "position": 21 + }, + { + "mutation": "C44T", + "count": 292, + "proportion": 0.5367647058823529, + "sequenceName": null, + "mutationFrom": "C", + "mutationTo": "T", + "position": 44 + }, + { + "mutation": "C241T", + "count": 2820, + "proportion": 0.9985835694050992, + "sequenceName": null, + "mutationFrom": "C", + "mutationTo": "T", + "position": 241 + }, + { + "mutation": "G515-", + "count": 157, + 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"count": 1897, + "proportion": 0.9688457609805925, + "sequenceName": null, + "mutationFrom": "C", + "mutationTo": "-", + "position": 29754 + }, + { + "mutation": "G29755-", + "count": 1897, + "proportion": 0.9688457609805925, + "sequenceName": null, + "mutationFrom": "G", + "mutationTo": "-", + "position": 29755 + }, + { + "mutation": "A29756-", + "count": 1897, + "proportion": 0.9688457609805925, + "sequenceName": null, + "mutationFrom": "A", + "mutationTo": "-", + "position": 29756 + }, + { + "mutation": "G29757-", + "count": 1897, + "proportion": 0.9688457609805925, + "sequenceName": null, + "mutationFrom": "G", + "mutationTo": "-", + "position": 29757 + }, + { + "mutation": "T29758-", + "count": 1897, + "proportion": 0.9688457609805925, + "sequenceName": null, + "mutationFrom": "T", + "mutationTo": "-", + "position": 29758 + }, + { + "mutation": "G29759-", + "count": 1896, + "proportion": 0.9683350357507661, + "sequenceName": null, + "mutationFrom": "G", + "mutationTo": "-", + "position": 29759 + } + ], + "info": { + "dataVersion": "1720033519", + "requestId": "3f36cdd2-49ba-41ce-92ec-43dfa1c30e1e", + "requestInfo": "sars_cov-2_nextstrain_open on lapis.cov-spectrum.org at 2024-07-17T14:53:28.677114291", + "reportTo": "Please report to https://github.com/GenSpectrum/LAPIS/issues in case you encounter any unexpected issues. Please include the request ID and the requestInfo in your report." + } +} diff --git a/components/src/preact/mutationOverTime/__mockData__/nucleotideMutations_2024_07.json b/components/src/preact/mutationOverTime/__mockData__/nucleotideMutations_2024_07.json new file mode 100644 index 00000000..7e0d9e90 --- /dev/null +++ b/components/src/preact/mutationOverTime/__mockData__/nucleotideMutations_2024_07.json @@ -0,0 +1,9 @@ +{ + "data": [], + "info": { + "dataVersion": "1720033519", + "requestId": "4701b007-bce8-49cf-b417-035785c0273b", + "requestInfo": "sars_cov-2_nextstrain_open on lapis.cov-spectrum.org at 2024-07-17T14:53:28.668667270", + "reportTo": "Please report to https://github.com/GenSpectrum/LAPIS/issues in case you encounter any unexpected issues. Please include the request ID and the requestInfo in your report." + } +} diff --git a/components/src/preact/mutationOverTime/mutation-over-time-grid.tsx b/components/src/preact/mutationOverTime/mutation-over-time-grid.tsx new file mode 100644 index 00000000..8cc652b1 --- /dev/null +++ b/components/src/preact/mutationOverTime/mutation-over-time-grid.tsx @@ -0,0 +1,92 @@ +import { Fragment, type FunctionComponent } from 'preact'; + +import { + type MutationOverTimeDataGroupedByMutation, + type MutationOverTimeMutationValue, +} from '../../query/queryMutationOverTime'; +import { type Deletion, type Substitution } from '../../utils/mutations'; +import { compareTemporal, type Temporal } from '../../utils/temporal'; +import { singleGraphColorRGBByName } from '../shared/charts/colors'; +import { formatProportion } from '../shared/table/formatProportion'; + +export interface MutationOverTimeGridProps { + data: MutationOverTimeDataGroupedByMutation; +} + +const MutationOverTimeGrid: FunctionComponent = ({ data }) => { + const mutations = data.getFirstAxisKeys(); + const dates = data.getSecondAxisKeys().sort((a, b) => compareTemporal(a, b)); + + return ( +
+ {mutations.map((mutation, i) => { + return ( + +
+ +
+ {dates.map((date, j) => { + const value = data.get(mutation, date) ?? 0; + return ( +
+ +
+ ); + })} + + ); + })} +
+ ); +}; + +const ProportionCell: FunctionComponent<{ + value: MutationOverTimeMutationValue; + date: Temporal; + mutation: Substitution | Deletion; +}> = ({ value }) => { + // TODO(#353): Add tooltip with date, mutation and proportion + return ( + <> +
+
+ {formatProportion(value, 0)} +
+
+ + ); +}; + +const backgroundColor = (proportion: number) => { + // TODO(#353): Make minAlpha and maxAlpha configurable + const minAlpha = 0.0; + const maxAlpha = 1; + + const alpha = minAlpha + (maxAlpha - minAlpha) * proportion; + return singleGraphColorRGBByName('indigo', alpha); +}; + +const textColor = (proportion: number) => { + return proportion > 0.5 ? 'white' : 'black'; +}; + +const MutationCell: FunctionComponent<{ mutation: Substitution | Deletion }> = ({ mutation }) => { + return
{mutation.toString()}
; +}; + +export default MutationOverTimeGrid; diff --git a/components/src/preact/mutationOverTime/mutation-over-time.stories.tsx b/components/src/preact/mutationOverTime/mutation-over-time.stories.tsx new file mode 100644 index 00000000..a4ecf352 --- /dev/null +++ b/components/src/preact/mutationOverTime/mutation-over-time.stories.tsx @@ -0,0 +1,199 @@ +import { type Meta, type StoryObj } from '@storybook/preact'; + +import aggregated_date from './__mockData__/aggregated_date.json'; +import nucleotideMutation_01 from './__mockData__/nucleotideMutations_2024_01.json'; +import nucleotideMutation_02 from './__mockData__/nucleotideMutations_2024_02.json'; +import nucleotideMutation_03 from './__mockData__/nucleotideMutations_2024_03.json'; +import nucleotideMutation_04 from './__mockData__/nucleotideMutations_2024_04.json'; +import nucleotideMutation_05 from './__mockData__/nucleotideMutations_2024_05.json'; +import nucleotideMutation_06 from './__mockData__/nucleotideMutations_2024_06.json'; +import nucleotideMutation_07 from './__mockData__/nucleotideMutations_2024_07.json'; +import { MutationOverTime, type MutationOverTimeProps } from './mutation-over-time'; +import { AGGREGATED_ENDPOINT, LAPIS_URL, NUCLEOTIDE_MUTATIONS_ENDPOINT } from '../../constants'; +import referenceGenome from '../../lapisApi/__mockData__/referenceGenome.json'; +import { LapisUrlContext } from '../LapisUrlContext'; +import { ReferenceGenomeContext } from '../ReferenceGenomeContext'; + +const meta: Meta = { + title: 'Visualization/Mutation over time', + component: MutationOverTime, + argTypes: { + lapisFilter: { control: 'object' }, + sequenceType: { + options: ['nucleotide', 'amino acid'], + control: { type: 'radio' }, + }, + views: { + options: ['table', 'grid', 'insertions'], + control: { type: 'check' }, + }, + width: { control: 'text' }, + height: { control: 'text' }, + headline: { control: 'text' }, + granularity: { + options: ['day', 'week', 'month', 'year'], + control: { type: 'radio' }, + }, + }, +}; + +export default meta; + +const Template = { + render: (args: MutationOverTimeProps) => ( + + + + + + ), +}; + +export const Default: StoryObj = { + ...Template, + args: { + lapisFilter: { pangoLineage: 'JN.1*', dateFrom: '2024-01-15', dateTo: '2024-07-10' }, + sequenceType: 'nucleotide', + views: ['grid'], + width: '100%', + height: '700px', + headline: 'Mutation over time', + granularity: 'month', + }, + parameters: { + fetchMock: { + mocks: [ + { + matcher: { + name: 'aggregated_dates', + url: AGGREGATED_ENDPOINT, + body: { + dateFrom: '2024-01-15', + dateTo: '2024-07-10', + fields: ['date'], + pangoLineage: 'JN.1*', + }, + }, + response: { + status: 200, + body: aggregated_date, + }, + }, + { + matcher: { + name: 'nucleotideMutations_01', + url: NUCLEOTIDE_MUTATIONS_ENDPOINT, + body: { + pangoLineage: 'JN.1*', + dateFrom: '2024-01-01', + dateTo: '2024-01-31', + }, + }, + response: { + status: 200, + body: nucleotideMutation_01, + }, + }, + { + matcher: { + name: 'nucleotideMutations_02', + url: NUCLEOTIDE_MUTATIONS_ENDPOINT, + body: { + pangoLineage: 'JN.1*', + dateFrom: '2024-02-01', + dateTo: '2024-02-29', + }, + }, + response: { + status: 200, + body: nucleotideMutation_02, + }, + }, + { + matcher: { + name: 'nucleotideMutations_03', + url: NUCLEOTIDE_MUTATIONS_ENDPOINT, + body: { + pangoLineage: 'JN.1*', + dateFrom: '2024-03-01', + dateTo: '2024-03-31', + }, + response: { + status: 200, + body: nucleotideMutation_03, + }, + }, + }, + { + matcher: { + name: 'nucleotideMutations_04', + url: NUCLEOTIDE_MUTATIONS_ENDPOINT, + body: { + pangoLineage: 'JN.1*', + dateFrom: '2024-04-01', + dateTo: '2024-04-30', + }, + response: { + status: 200, + body: nucleotideMutation_04, + }, + }, + }, + { + matcher: { + name: 'nucleotideMutations_05', + url: NUCLEOTIDE_MUTATIONS_ENDPOINT, + body: { + pangoLineage: 'JN.1*', + dateFrom: '2024-05-01', + dateTo: '2024-05-31', + }, + response: { + status: 200, + body: nucleotideMutation_05, + }, + }, + }, + { + matcher: { + name: 'nucleotideMutations_06', + url: NUCLEOTIDE_MUTATIONS_ENDPOINT, + body: { + pangoLineage: 'JN.1*', + dateFrom: '2024-06-01', + dateTo: '2024-06-30', + }, + response: { + status: 200, + body: nucleotideMutation_06, + }, + }, + }, + + { + matcher: { + name: 'nucleotideMutations_07', + url: NUCLEOTIDE_MUTATIONS_ENDPOINT, + body: { + pangoLineage: 'JN.1*', + dateFrom: '2024-07-01', + dateTo: '2024-07-31', + }, + response: { + status: 200, + body: nucleotideMutation_07, + }, + }, + }, + ], + }, + }, +}; diff --git a/components/src/preact/mutationOverTime/mutation-over-time.tsx b/components/src/preact/mutationOverTime/mutation-over-time.tsx new file mode 100644 index 00000000..4a613d8a --- /dev/null +++ b/components/src/preact/mutationOverTime/mutation-over-time.tsx @@ -0,0 +1,184 @@ +import { type FunctionComponent } from 'preact'; +import { type Dispatch, type StateUpdater, useContext, useMemo, useState } from 'preact/hooks'; + +import MutationOverTimeGrid from './mutation-over-time-grid'; +import { + filterMutationOverTimeData, + type MutationOverTimeDataGroupedByMutation, + queryMutationOverTimeData, +} from '../../query/queryMutationOverTime'; +import { type LapisFilter, type SequenceType, type TemporalGranularity } from '../../types'; +import { LapisUrlContext } from '../LapisUrlContext'; +import { type DisplayedSegment, SegmentSelector, useDisplayedSegments } from '../components/SegmentSelector'; +import { CsvDownloadButton } from '../components/csv-download-button'; +import { ErrorBoundary } from '../components/error-boundary'; +import { ErrorDisplay } from '../components/error-display'; +import Headline from '../components/headline'; +import Info from '../components/info'; +import { LoadingDisplay } from '../components/loading-display'; +import { type DisplayedMutationType, MutationTypeSelector } from '../components/mutation-type-selector'; +import { NoDataDisplay } from '../components/no-data-display'; +import type { ProportionInterval } from '../components/proportion-selector'; +import { ProportionSelectorDropdown } from '../components/proportion-selector-dropdown'; +import { ResizeContainer } from '../components/resize-container'; +import Tabs from '../components/tabs'; +import { useQuery } from '../useQuery'; + +export type View = 'grid'; + +export interface MutationOverTimeInnerProps { + lapisFilter: LapisFilter; + sequenceType: SequenceType; + views: View[]; + granularity: TemporalGranularity; +} + +export interface MutationOverTimeProps extends MutationOverTimeInnerProps { + width: string; + height: string; + headline?: string; +} + +export const MutationOverTime: FunctionComponent = ({ + width, + height, + headline = 'Mutation over time', + ...innerProps +}) => { + const size = { height, width }; + + return ( + + + + + + + + ); +}; + +export const MutationOverTimeInner: FunctionComponent = ({ + lapisFilter, + sequenceType, + views, + granularity, +}) => { + const lapis = useContext(LapisUrlContext); + const { data, error, isLoading } = useQuery(async () => { + return queryMutationOverTimeData(lapisFilter, sequenceType, lapis, 'date', granularity); + }, [lapisFilter, sequenceType, lapis]); + + if (isLoading) { + return ; + } + + if (error !== null) { + return ; + } + + if (data === null) { + return ; + } + + return ; +}; + +type MutationOverTimeTabsProps = { + mutationOverTimeData: MutationOverTimeDataGroupedByMutation; + sequenceType: SequenceType; + views: View[]; +}; + +const MutationOverTimeTabs: FunctionComponent = ({ + mutationOverTimeData, + sequenceType, + views, +}) => { + const [proportionInterval, setProportionInterval] = useState({ min: 0.05, max: 0.9 }); + + const [displayedSegments, setDisplayedSegments] = useDisplayedSegments(sequenceType); + const [displayedMutationTypes, setDisplayedMutationTypes] = useState([ + { label: 'Substitutions', checked: true, type: 'substitution' }, + { label: 'Deletions', checked: true, type: 'deletion' }, + ]); + + const filteredData = useMemo( + () => + filterMutationOverTimeData( + mutationOverTimeData.copy(), + displayedSegments, + displayedMutationTypes, + proportionInterval, + ), + [mutationOverTimeData, displayedSegments, displayedMutationTypes, proportionInterval], + ); + + const getTab = (view: View) => { + switch (view) { + case 'grid': + return { + title: 'Grid', + content: , + }; + } + }; + + const tabs = views.map((view) => getTab(view)); + + const toolbar = () => ( + + ); + + return ; +}; + +type ToolbarProps = { + displayedSegments: DisplayedSegment[]; + setDisplayedSegments: (segments: DisplayedSegment[]) => void; + displayedMutationTypes: DisplayedMutationType[]; + setDisplayedMutationTypes: (types: DisplayedMutationType[]) => void; + proportionInterval: ProportionInterval; + setProportionInterval: Dispatch>; +}; + +const Toolbar: FunctionComponent = ({ + displayedSegments, + setDisplayedSegments, + displayedMutationTypes, + setDisplayedMutationTypes, + proportionInterval, + setProportionInterval, +}) => { + return ( + <> + + + <> + setProportionInterval((prev) => ({ ...prev, min }))} + setMaxProportion={(max) => setProportionInterval((prev) => ({ ...prev, max }))} + /> + { + return [{ value: 1 }, { value: 2 }]; + }} + filename='mutation-over-time.csv' + /> + + Info for mutation over time + + ); +}; diff --git a/components/src/preact/numberSequencesOverTime/getNumberOfSequencesOverTimeTableData.ts b/components/src/preact/numberSequencesOverTime/getNumberOfSequencesOverTimeTableData.ts index aeb33d91..b05244dc 100644 --- a/components/src/preact/numberSequencesOverTime/getNumberOfSequencesOverTimeTableData.ts +++ b/components/src/preact/numberSequencesOverTime/getNumberOfSequencesOverTimeTableData.ts @@ -21,7 +21,7 @@ export const getNumberOfSequencesOverTimeTableData = { - return `${(proportion * 100).toFixed(2)}%`; +export const formatProportion = (proportion: number, digits: number = 2) => { + return `${(proportion * 100).toFixed(digits)}%`; }; diff --git a/components/src/query/queryAggregatedDataOverTime.ts b/components/src/query/queryAggregatedDataOverTime.ts index a9e14249..961e3078 100644 --- a/components/src/query/queryAggregatedDataOverTime.ts +++ b/components/src/query/queryAggregatedDataOverTime.ts @@ -6,13 +6,7 @@ import { RenameFieldOperator } from '../operator/RenameFieldOperator'; import { SlidingOperator } from '../operator/SlidingOperator'; import { SortOperator } from '../operator/SortOperator'; import type { LapisFilter, TemporalGranularity } from '../types'; -import { - compareTemporal, - generateAllInRange, - getMinMaxTemporal, - type Temporal, - TemporalCache, -} from '../utils/temporal'; +import { compareTemporal, generateAllInRange, getMinMaxTemporal, parseDate, type Temporal } from '../utils/temporal'; export function queryAggregatedDataOverTime( filter: LapisFilter, @@ -36,32 +30,17 @@ export function queryAggregatedDataOverTime( return smoothingWindow >= 1 ? new SlidingOperator(sortData, smoothingWindow, averageSmoothing) : sortData; } -function mapDateToGranularityRange(d: { date: string | null; count: number }, granularity: TemporalGranularity) { - let dateRange: Temporal | null = null; - if (d.date !== null) { - const date = TemporalCache.getInstance().getYearMonthDay(d.date); - switch (granularity) { - case 'day': - dateRange = date; - break; - case 'week': - dateRange = date.week; - break; - case 'month': - dateRange = date.month; - break; - case 'year': - dateRange = date.year; - break; - } - } +export function mapDateToGranularityRange( + data: { date: string | null; count: number }, + granularity: TemporalGranularity, +) { return { - dateRange, - count: d.count, + dateRange: data.date === null ? null : parseDate(data.date, granularity), + count: data.count, }; } -function dateRangeCompare(a: { dateRange: Temporal | null }, b: { dateRange: Temporal | null }) { +export function dateRangeCompare(a: { dateRange: Temporal | null }, b: { dateRange: Temporal | null }) { if (a.dateRange === null) { return 1; } diff --git a/components/src/query/queryMutationOverTime.ts b/components/src/query/queryMutationOverTime.ts new file mode 100644 index 00000000..e3c90e1d --- /dev/null +++ b/components/src/query/queryMutationOverTime.ts @@ -0,0 +1,219 @@ +import { dateRangeCompare, mapDateToGranularityRange } from './queryAggregatedDataOverTime'; +import { FetchAggregatedOperator } from '../operator/FetchAggregatedOperator'; +import { FetchSubstitutionsOrDeletionsOperator } from '../operator/FetchSubstitutionsOrDeletionsOperator'; +import { GroupByAndSumOperator } from '../operator/GroupByAndSumOperator'; +import { MapOperator } from '../operator/MapOperator'; +import { RenameFieldOperator } from '../operator/RenameFieldOperator'; +import { SortOperator } from '../operator/SortOperator'; +import type { DisplayedSegment } from '../preact/components/SegmentSelector'; +import type { DisplayedMutationType } from '../preact/components/mutation-type-selector'; +import { + type LapisFilter, + type SequenceType, + type SubstitutionOrDeletionEntry, + type TemporalGranularity, +} from '../types'; +import { Map2d } from '../utils/Map2d'; +import { type Deletion, type Substitution } from '../utils/mutations'; +import { generateAllInRange, getMinMaxTemporal, parseDate, type Temporal } from '../utils/temporal'; + +export type MutationOverTimeData = { + date: Temporal; + mutations: SubstitutionOrDeletionEntry[]; +}; + +export type MutationOverTimeMutationValue = number; +export type MutationOverTimeDataGroupedByMutation = Map2d< + Substitution | Deletion, + Temporal, + MutationOverTimeMutationValue +>; + +export async function queryMutationOverTimeData( + lapisFilter: LapisFilter, + sequenceType: 'nucleotide' | 'amino acid', + lapis: string, + lapisDateField: string, + granularity: TemporalGranularity, + signal?: AbortSignal, +) { + const allDates = await getDatesInDataset(lapisFilter, lapis, granularity, lapisDateField, signal); + + const subQueries = allDates.map(async (date) => { + const dateFrom = date.firstDay.toString(); + const dateTo = date.lastDay.toString(); + + const filter = { + ...lapisFilter, + [`${lapisDateField}From`]: dateFrom, + [`${lapisDateField}To`]: dateTo, + }; + + const data = await fetchAndPrepare(filter, sequenceType).evaluate(lapis, signal); + return { + date, + mutations: data.content, + }; + }); + + const data = await Promise.all(subQueries); + + return groupByMutation(data); +} + +async function getDatesInDataset( + lapisFilter: LapisFilter, + lapis: string, + granularity: 'day' | 'week' | 'month' | 'year', + lapisDateField: string, + signal: AbortSignal | undefined, +) { + const { content: availableDates } = await queryAvailableDates( + lapisFilter, + lapis, + granularity, + lapisDateField, + signal, + ); + + const { dateFrom, dateTo } = getDateRangeFromFilter(lapisFilter, lapisDateField, granularity); + const { min, max } = getMinMaxTemporal([...availableDates, dateFrom, dateTo]); + return generateAllInRange(min, max); +} + +function getDateRangeFromFilter(lapisFilter: LapisFilter, lapisDateField: string, granularity: TemporalGranularity) { + const valueFromFilter = lapisFilter[lapisDateField] as string | null; + + if (valueFromFilter) { + return { + dateFrom: parseDate(valueFromFilter, granularity), + dateTo: parseDate(valueFromFilter, granularity), + }; + } + + const minFromFilter = lapisFilter[`${lapisDateField}From`] as string | null; + const maxFromFilter = lapisFilter[`${lapisDateField}To`] as string | null; + + return { + dateFrom: minFromFilter ? parseDate(minFromFilter, granularity) : null, + dateTo: maxFromFilter ? parseDate(maxFromFilter, granularity) : null, + }; +} + +function queryAvailableDates( + lapisFilter: LapisFilter, + lapis: string, + granularity: TemporalGranularity, + lapisDateField: string, + signal?: AbortSignal, +) { + return fetchAndPrepareDates(lapisFilter, granularity, lapisDateField).evaluate(lapis, signal); +} + +function fetchAndPrepareDates( + filter: LapisFilter, + granularity: TemporalGranularity, + lapisDateField: LapisDateField, +) { + const fetchData = new FetchAggregatedOperator<{ [key in LapisDateField]: string | null }>(filter, [lapisDateField]); + const dataWithFixedDateKey = new RenameFieldOperator(fetchData, lapisDateField, 'date'); + const mapData = new MapOperator(dataWithFixedDateKey, (data) => mapDateToGranularityRange(data, granularity)); + const groupByData = new GroupByAndSumOperator(mapData, 'dateRange', 'count'); + const sortData = new SortOperator(groupByData, dateRangeCompare); + return new MapOperator(sortData, (data) => data.dateRange); +} + +function fetchAndPrepare(filter: LapisFilter, sequenceType: SequenceType) { + return new FetchSubstitutionsOrDeletionsOperator(filter, sequenceType); +} + +export function filterMutationOverTimeData( + data: Map2d, + displayedSegments: DisplayedSegment[], + displayedMutationTypes: DisplayedMutationType[], + proportionInterval: { min: number; max: number }, +) { + filterDisplayedSegments(displayedSegments, data); + filterMutationTypes(displayedMutationTypes, data); + filterProportion(data, proportionInterval); + + return data; +} + +function filterDisplayedSegments( + displayedSegments: DisplayedSegment[], + data: Map2d, +) { + displayedSegments.forEach((segment) => { + if (!segment.checked) { + data.getFirstAxisKeys().forEach((mutation) => { + if (mutation.segment === segment.segment) { + data.deleteRow(mutation); + } + }); + } + }); +} + +function filterMutationTypes( + displayedMutationTypes: DisplayedMutationType[], + data: Map2d, +) { + displayedMutationTypes.forEach((mutationType) => { + if (!mutationType.checked) { + data.getFirstAxisKeys().forEach((mutation) => { + if (mutationType.type === mutation.type) { + data.deleteRow(mutation); + } + }); + } + }); +} + +function filterProportion( + data: Map2d, + proportionInterval: { + min: number; + max: number; + }, +) { + data.getFirstAxisKeys().forEach((mutation) => { + const row = data.getRow(mutation, 0); + if ( + !row.some((value) => { + return value >= proportionInterval.min && value <= proportionInterval.max; + }) + ) { + data.deleteRow(mutation); + } + }); +} + +export function groupByMutation(data: MutationOverTimeData[]) { + const dataArray = new Map2d( + (mutation) => mutation.code, + (date) => date.toString(), + ); + + data.forEach((mutationData) => { + mutationData.mutations.forEach((mutationEntry) => { + dataArray.set(mutationEntry.mutation, mutationData.date, mutationEntry.proportion); + }); + }); + + addZeroValuesForDatesWithNoMutationData(dataArray, data); + + return dataArray; +} + +function addZeroValuesForDatesWithNoMutationData( + dataArray: Map2d, + data: MutationOverTimeData[], +) { + const someMutation = dataArray.getFirstAxisKeys()[0]; + data.forEach((mutationData) => { + if (mutationData.mutations.length === 0) { + dataArray.set(someMutation, mutationData.date, 0); + } + }); +} diff --git a/components/src/query/queryNumberOfSequencesOverTime.ts b/components/src/query/queryNumberOfSequencesOverTime.ts index c200ed2a..aabdcbff 100644 --- a/components/src/query/queryNumberOfSequencesOverTime.ts +++ b/components/src/query/queryNumberOfSequencesOverTime.ts @@ -4,7 +4,6 @@ import { sortNullToBeginningThenByDate } from '../utils/sort'; import { makeArray } from '../utils/utils'; export type NumberOfSequencesDatasets = Awaited>; -export type NumberOfSequencesDataset = NumberOfSequencesDatasets[number]; export async function queryNumberOfSequencesOverTime( lapis: string, diff --git a/components/src/query/queryRelativeGrowthAdvantage.ts b/components/src/query/queryRelativeGrowthAdvantage.ts index 158b83e2..f93623a6 100644 --- a/components/src/query/queryRelativeGrowthAdvantage.ts +++ b/components/src/query/queryRelativeGrowthAdvantage.ts @@ -28,11 +28,13 @@ export async function queryRelativeGrowthAdvantage d.date)); - if (!minMaxDate) { + const { min, max } = getMinMaxTemporal(denominatorData.content.map((d) => d.date)); + if (!min && !max) { return null; } - const [minDate, maxDate] = minMaxDate as [YearMonthDay, YearMonthDay]; + const minDate = min as YearMonthDay; + const maxDate = max as YearMonthDay; + const numeratorCounts = new Map(); numeratorData.content.forEach((d) => { if (d.date) { diff --git a/components/src/utils/Map2d.ts b/components/src/utils/Map2d.ts new file mode 100644 index 00000000..39b20fe7 --- /dev/null +++ b/components/src/utils/Map2d.ts @@ -0,0 +1,75 @@ +import hash from 'object-hash'; + +export class Map2d { + readonly data: Map> = new Map>(); + readonly keysFirstAxis = new Map(); + readonly keysSecondAxis = new Map(); + + constructor( + readonly serializeFirstAxis: (key: Key1) => string = (key) => (typeof key === 'string' ? key : hash(key)), + readonly serializeSecondAxis: (key: Key2) => string = (key) => (typeof key === 'string' ? key : hash(key)), + ) {} + + get(keyFirstAxis: Key1, keySecondAxis: Key2) { + const serializedKeyFirstAxis = this.serializeFirstAxis(keyFirstAxis); + const serializedKeySecondAxis = this.serializeSecondAxis(keySecondAxis); + return this.data.get(serializedKeyFirstAxis)?.get(serializedKeySecondAxis); + } + + getRow(key: Key1, fillEmptyWith: Value) { + const serializedKeyFirstAxis = this.serializeFirstAxis(key); + const row = this.data.get(serializedKeyFirstAxis); + if (row === undefined) { + return []; + } + return Array.from(this.keysSecondAxis.keys()).map((key) => row.get(key) ?? fillEmptyWith); + } + + set(keyFirstAxis: Key1, keySecondAxis: Key2, value: Value) { + const serializedKeyFirstAxis = this.serializeFirstAxis(keyFirstAxis); + const serializedKeySecondAxis = this.serializeSecondAxis(keySecondAxis); + + if (!this.data.has(serializedKeyFirstAxis)) { + this.data.set(serializedKeyFirstAxis, new Map()); + } + + this.data.get(serializedKeyFirstAxis)!.set(serializedKeySecondAxis, value); + + this.keysFirstAxis.set(serializedKeyFirstAxis, keyFirstAxis); + this.keysSecondAxis.set(serializedKeySecondAxis, keySecondAxis); + } + + deleteRow(key: Key1) { + const serializedKeyFirstAxis = this.serializeFirstAxis(key); + this.data.delete(serializedKeyFirstAxis); + this.keysFirstAxis.delete(serializedKeyFirstAxis); + } + + getFirstAxisKeys() { + return Array.from(this.keysFirstAxis.values()); + } + + getSecondAxisKeys() { + return Array.from(this.keysSecondAxis.values()); + } + + getAsArray(fillEmptyWith: Value) { + return this.getFirstAxisKeys().map((firstAxisKey) => { + return this.getSecondAxisKeys().map((secondAxisKey) => { + return this.get(firstAxisKey, secondAxisKey) ?? fillEmptyWith; + }); + }); + } + + copy() { + const copy = new Map2d(this.serializeFirstAxis, this.serializeSecondAxis); + this.data.forEach((value, key) => { + const keyFirstAxis = this.keysFirstAxis.get(key); + value.forEach((value, key) => { + const keySecondAxis = this.keysSecondAxis.get(key); + copy.set(keyFirstAxis!, keySecondAxis!, value); + }); + }); + return copy; + } +} diff --git a/components/src/utils/map2d.spec.ts b/components/src/utils/map2d.spec.ts new file mode 100644 index 00000000..bcb9679c --- /dev/null +++ b/components/src/utils/map2d.spec.ts @@ -0,0 +1,94 @@ +import { describe, expect, it } from 'vitest'; + +import { Map2d } from './Map2d'; + +describe('Map2d', () => { + it('should add a value and return it', () => { + const map2d = new Map2d(); + map2d.set('a', 'b', 2); + expect(map2d.get('a', 'b')).toBe(2); + }); + + it('should update a value', () => { + const map2d = new Map2d(); + map2d.set('a', 'b', 2); + map2d.set('a', 'b', 3); + expect(map2d.get('a', 'b')).toBe(3); + }); + + it('should return the data as an array', () => { + const map2d = new Map2d(); + map2d.set('a', 'b', 1); + map2d.set('a', 'd', 2); + map2d.set('c', 'b', 3); + map2d.set('c', 'd', 4); + + expect(map2d.getAsArray(0)).toEqual([ + [1, 2], + [3, 4], + ]); + }); + + it('should fill empty values with the given value', () => { + const map2d = new Map2d(); + map2d.set('a', 'b', 2); + map2d.set('c', 'd', 4); + expect(map2d.getAsArray(0)).toEqual([ + [2, 0], + [0, 4], + ]); + }); + + it('should return the keys from the first axis', () => { + const map2d = new Map2d(); + map2d.set('a', 'b', 2); + map2d.set('c', 'd', 4); + + expect(map2d.getFirstAxisKeys()).toEqual(['a', 'c']); + }); + + it('should return the keys from the second axis', () => { + const map2d = new Map2d(); + map2d.set('a', 'b', 2); + map2d.set('c', 'd', 4); + + expect(map2d.getSecondAxisKeys()).toEqual(['b', 'd']); + }); + + it('should work with objects as keys', () => { + const map2d = new Map2d<{ a: string }, { b: string }, number>(); + map2d.set({ a: 'a' }, { b: 'b' }, 2); + map2d.set({ a: 'second' }, { b: 'second' }, 3); + + expect(map2d.get({ a: 'a' }, { b: 'b' })).toBe(2); + expect(map2d.get({ a: 'second' }, { b: 'second' })).toBe(3); + }); + + it('should update a value with objects as keys', () => { + const map2d = new Map2d<{ a: string }, { b: string }, number>(); + map2d.set({ a: 'a' }, { b: 'b' }, 2); + map2d.set({ a: 'a' }, { b: 'b' }, 3); + expect(map2d.get({ a: 'a' }, { b: 'b' })).toBe(3); + }); + + it('should create a deep copy of the map', () => { + const map2d = new Map2d(); + map2d.set('a', 'b', 2); + expect(map2d.get('a', 'b')).toBe(2); + + const copy = map2d.copy(); + expect(copy.get('a', 'b')).toBe(2); + + map2d.deleteRow('a'); + expect(map2d.get('a', 'b')).toBe(undefined); + }); + + it('should return a row by key', () => { + const map2d = new Map2d(); + map2d.set('a', 'b', 2); + map2d.set('c', 'd', 4); + + expect(map2d.getRow('a', 0)).toEqual([2, 0]); + expect(map2d.getRow('c', 0)).toEqual([0, 4]); + }); +}); diff --git a/components/src/utils/mutations.ts b/components/src/utils/mutations.ts index 6fd02870..a2a8c440 100644 --- a/components/src/utils/mutations.ts +++ b/components/src/utils/mutations.ts @@ -1,9 +1,10 @@ -import { type SequenceType } from '../types'; +import { type MutationType, type SequenceType } from '../types'; export interface Mutation { readonly segment: string | undefined; readonly position: number; readonly code: string; + readonly type: MutationType; equals(other: Mutation): boolean; @@ -15,6 +16,7 @@ export const substitutionRegex = export class Substitution implements Mutation { readonly code; + readonly type = 'substitution'; constructor( readonly segment: string | undefined, @@ -62,6 +64,7 @@ export const deletionRegex = /^((?[A-Za-z0-9_-]+)(?=:):)?(?): [Temporal, Temporal] | null { +export function getMinMaxTemporal(values: Iterable) { let min = null; let max = null; for (const value of values) { @@ -326,9 +360,9 @@ export function getMinMaxTemporal(values: Iterable): [Temporal, } } if (min === null || max === null) { - return null; + return { min: null, max: null }; } - return [min, max]; + return { min, max }; } export function addUnit(temporal: Temporal, amount: number): Temporal { @@ -346,3 +380,18 @@ export function addUnit(temporal: Temporal, amount: number): Temporal { } throw new Error(`Invalid argument: ${temporal}`); } + +export function parseDate(date: string, granularity: TemporalGranularity) { + const cache = TemporalCache.getInstance(); + const day = cache.getYearMonthDay(date); + switch (granularity) { + case 'day': + return day; + case 'week': + return day.week; + case 'month': + return day.month; + case 'year': + return day.year; + } +} diff --git a/components/src/web-components/visualization/gs-mutation-over-time.stories.ts b/components/src/web-components/visualization/gs-mutation-over-time.stories.ts new file mode 100644 index 00000000..d387b674 --- /dev/null +++ b/components/src/web-components/visualization/gs-mutation-over-time.stories.ts @@ -0,0 +1,216 @@ +import type { Meta, StoryObj } from '@storybook/web-components'; +import { html } from 'lit'; + +import './gs-mutation-over-time'; +import '../app'; +import { withComponentDocs } from '../../../.storybook/ComponentDocsBlock'; +import { AGGREGATED_ENDPOINT, LAPIS_URL, NUCLEOTIDE_MUTATIONS_ENDPOINT } from '../../constants'; +import aggregated_date from '../../preact/mutationOverTime/__mockData__/aggregated_date.json'; +import nucleotideMutation_01 from '../../preact/mutationOverTime/__mockData__/nucleotideMutations_2024_01.json'; +import nucleotideMutation_02 from '../../preact/mutationOverTime/__mockData__/nucleotideMutations_2024_02.json'; +import nucleotideMutation_03 from '../../preact/mutationOverTime/__mockData__/nucleotideMutations_2024_03.json'; +import nucleotideMutation_04 from '../../preact/mutationOverTime/__mockData__/nucleotideMutations_2024_04.json'; +import nucleotideMutation_05 from '../../preact/mutationOverTime/__mockData__/nucleotideMutations_2024_05.json'; +import nucleotideMutation_06 from '../../preact/mutationOverTime/__mockData__/nucleotideMutations_2024_06.json'; +import nucleotideMutation_07 from '../../preact/mutationOverTime/__mockData__/nucleotideMutations_2024_07.json'; +import { type MutationOverTimeProps } from '../../preact/mutationOverTime/mutation-over-time'; + +const codeExample = String.raw` +`; + +const meta: Meta> = { + title: 'Visualization/Mutation over time', + component: 'gs-mutation-over-time', + argTypes: { + lapisFilter: { control: 'object' }, + sequenceType: { + options: ['nucleotide', 'amino acid'], + control: { type: 'radio' }, + }, + views: { + options: ['grid'], + control: { type: 'check' }, + }, + width: { control: 'text' }, + height: { control: 'text' }, + headline: { control: 'text' }, + granularity: { + options: ['day', 'week', 'month', 'year'], + control: { type: 'radio' }, + }, + }, + args: { + lapisFilter: { pangoLineage: 'JN.1*', dateFrom: '2024-01-15', dateTo: '2024-07-10' }, + sequenceType: 'nucleotide', + views: ['grid'], + width: '100%', + height: '700px', + headline: 'Mutation over time', + granularity: 'month', + }, + parameters: withComponentDocs({ + componentDocs: { + opensShadowDom: true, + expectsChildren: false, + codeExample, + }, + }), + tags: ['autodocs'], +}; + +export default meta; + +const Template: StoryObj> = { + render: (args) => html` + + + + `, +}; + +export const Default: StoryObj> = { + ...Template, + parameters: { + fetchMock: { + mocks: [ + { + matcher: { + name: 'aggregated_dates', + url: AGGREGATED_ENDPOINT, + body: { + dateFrom: '2024-01-15', + dateTo: '2024-07-10', + fields: ['date'], + pangoLineage: 'JN.1*', + }, + }, + response: { + status: 200, + body: aggregated_date, + }, + }, + { + matcher: { + name: 'nucleotideMutations_01', + url: NUCLEOTIDE_MUTATIONS_ENDPOINT, + body: { + pangoLineage: 'JN.1*', + dateFrom: '2024-01-01', + dateTo: '2024-01-31', + }, + }, + response: { + status: 200, + body: nucleotideMutation_01, + }, + }, + { + matcher: { + name: 'nucleotideMutations_02', + url: NUCLEOTIDE_MUTATIONS_ENDPOINT, + body: { + pangoLineage: 'JN.1*', + dateFrom: '2024-02-01', + dateTo: '2024-02-29', + }, + }, + response: { + status: 200, + body: nucleotideMutation_02, + }, + }, + { + matcher: { + name: 'nucleotideMutations_03', + url: NUCLEOTIDE_MUTATIONS_ENDPOINT, + body: { + pangoLineage: 'JN.1*', + dateFrom: '2024-03-01', + dateTo: '2024-03-31', + }, + response: { + status: 200, + body: nucleotideMutation_03, + }, + }, + }, + { + matcher: { + name: 'nucleotideMutations_04', + url: NUCLEOTIDE_MUTATIONS_ENDPOINT, + body: { + pangoLineage: 'JN.1*', + dateFrom: '2024-04-01', + dateTo: '2024-04-30', + }, + response: { + status: 200, + body: nucleotideMutation_04, + }, + }, + }, + { + matcher: { + name: 'nucleotideMutations_05', + url: NUCLEOTIDE_MUTATIONS_ENDPOINT, + body: { + pangoLineage: 'JN.1*', + dateFrom: '2024-05-01', + dateTo: '2024-05-31', + }, + response: { + status: 200, + body: nucleotideMutation_05, + }, + }, + }, + { + matcher: { + name: 'nucleotideMutations_06', + url: NUCLEOTIDE_MUTATIONS_ENDPOINT, + body: { + pangoLineage: 'JN.1*', + dateFrom: '2024-06-01', + dateTo: '2024-06-30', + }, + response: { + status: 200, + body: nucleotideMutation_06, + }, + }, + }, + + { + matcher: { + name: 'nucleotideMutations_07', + url: NUCLEOTIDE_MUTATIONS_ENDPOINT, + body: { + pangoLineage: 'JN.1*', + dateFrom: '2024-07-01', + dateTo: '2024-07-31', + }, + response: { + status: 200, + body: nucleotideMutation_07, + }, + }, + }, + ], + }, + }, +}; diff --git a/components/src/web-components/visualization/gs-mutation-over-time.tsx b/components/src/web-components/visualization/gs-mutation-over-time.tsx new file mode 100644 index 00000000..f5208e30 --- /dev/null +++ b/components/src/web-components/visualization/gs-mutation-over-time.tsx @@ -0,0 +1,97 @@ +import { customElement, property } from 'lit/decorators.js'; + +import { MutationOverTime, type View } from '../../preact/mutationOverTime/mutation-over-time'; +import { type LapisFilter, type SequenceType } from '../../types'; +import type { Equals, Expect } from '../../utils/typeAssertions'; +import { PreactLitAdapterWithGridJsStyles } from '../PreactLitAdapterWithGridJsStyles'; + +/** + * ## Context + * + * This component displays mutations (substitutions and deletions) over time for a dataset selected by a LAPIS filter. + * The shown date range is determined by the date field in the LAPIS filter. + * If the date field is not set, the date range is determined by all available dates in the dataset. + * + * ## Views + * + * ### Grid View + * + * The grid view shows the proportion for each mutation over date ranges. + * + */ +@customElement('gs-mutation-over-time') +export class MutationOverTimeComponent extends PreactLitAdapterWithGridJsStyles { + /** + * Required. + * + * LAPIS filter to select the displayed data. + */ + @property({ type: Object }) + lapisFilter: Record = {}; + + /** + * The type of the sequence for which the mutations should be shown. + */ + @property({ type: String }) + sequenceType: 'nucleotide' | 'amino acid' = 'nucleotide'; + + /** + * A list of tabs with views that this component should provide. + */ + @property({ type: Array }) + views: 'grid'[] = ['grid']; + + /** + * The width of the component. + * + * Visit https://genspectrum.github.io/dashboard-components/?path=/docs/components-size-of-components--docs for more information. + */ + @property({ type: String }) + width: string = '100%'; + + /** + * The height of the component. + * + * Visit https://genspectrum.github.io/dashboard-components/?path=/docs/components-size-of-components--docs for more information. + */ + @property({ type: String }) + height: string = '700px'; + + /** + * The headline of the component. Set to an empty string to hide the headline. + */ + @property({ type: String }) + headline: string = 'Mutation over time'; + + /** + * The granularity of the time axis. + */ + @property({ type: String }) + granularity: 'day' | 'week' | 'month' | 'year' = 'week'; + + override render() { + return ( + + ); + } +} + +declare global { + interface HTMLElementTagNameMap { + 'gs-mutation-over-time-component': MutationOverTimeComponent; + } +} + +/* eslint-disable @typescript-eslint/no-unused-vars, no-unused-vars */ +type LapisFilterMatches = Expect>; +type SequenceTypeMatches = Expect>; +type ViewsMatches = Expect>; +/* eslint-enable @typescript-eslint/no-unused-vars, no-unused-vars */ diff --git a/components/tests/snapshots.spec.ts-snapshots/Mutation-over-time-Story-visualization-mutation-over-time--default-should-match-screenshot-1-chromium-linux.png b/components/tests/snapshots.spec.ts-snapshots/Mutation-over-time-Story-visualization-mutation-over-time--default-should-match-screenshot-1-chromium-linux.png new file mode 100644 index 00000000..39c5c5fd Binary files /dev/null and b/components/tests/snapshots.spec.ts-snapshots/Mutation-over-time-Story-visualization-mutation-over-time--default-should-match-screenshot-1-chromium-linux.png differ diff --git a/components/tests/snapshots.spec.ts-snapshots/Mutation-over-time-Story-visualization-mutation-over-time--default-should-match-screenshot-1-firefox-linux.png b/components/tests/snapshots.spec.ts-snapshots/Mutation-over-time-Story-visualization-mutation-over-time--default-should-match-screenshot-1-firefox-linux.png new file mode 100644 index 00000000..3a6453cf Binary files /dev/null and b/components/tests/snapshots.spec.ts-snapshots/Mutation-over-time-Story-visualization-mutation-over-time--default-should-match-screenshot-1-firefox-linux.png differ diff --git a/components/tests/visualizationStories.ts b/components/tests/visualizationStories.ts index f18ccc6c..495bb697 100644 --- a/components/tests/visualizationStories.ts +++ b/components/tests/visualizationStories.ts @@ -42,4 +42,8 @@ export const visualizationStories = [ id: 'visualization-number-sequences-over-time--two-datasets-with-non-overlapping-dates', title: 'Number of sequences over time', }, + { + id: 'visualization-mutation-over-time--default', + title: 'Mutation over time', + }, ];