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NickAkhmetovNickAkhmetov
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Initial hooks for scfind + tests for URL hook param formatting
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‎context/app/static/js/api/scfind/scfind.test.ts

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import { createScfindKey, annotationNamesToGetParams, SCFIND_BASE } from './utils';
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describe('createScfindKey', () => {
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function expectURLIsValid(key: string) {
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expect(() => new URL(key)).not.toThrow();
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}
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it('should use the appropriate scfind base URL', () => {
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const key = createScfindKey('endpoint', {});
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expect(key).toContain(SCFIND_BASE);
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expectURLIsValid(key);
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});
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it.each(['endpoint1', 'endpoint2', 'endpoint3', 'my-weird-endpoint'])(
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'should use the appropriate provided endpoint',
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(endpoint) => {
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const key = createScfindKey(endpoint, {});
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expect(key).toContain(endpoint);
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expectURLIsValid(key);
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},
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);
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it.each([
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{
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params: {
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param1: 'value1',
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param2: 'value2',
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param3: undefined,
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},
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definedKeys: ['param1', 'param2'],
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undefinedKeys: ['param3'],
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},
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])('should filter out undefined passed params', ({ params, definedKeys, undefinedKeys }) => {
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const key = createScfindKey('endpoint', params);
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definedKeys.forEach((k) => {
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expect(key.includes(k));
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});
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undefinedKeys.forEach((k) => {
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expect(!key.includes(k));
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});
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expectURLIsValid(key);
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});
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});
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describe('annotationNamesToGetParams', () => {
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it('should return undefined if annotationNames is undefined', () => {
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expect(annotationNamesToGetParams(undefined)).toBeUndefined();
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});
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it.each([
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{
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obj: [
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{ Organ: 'organ1', Tissue: 'tissue1' },
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{ Organ: 'organ1', Tissue: 'tissue2' },
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],
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expected: '[{"Organ": "organ1", "Tissue": "tissue1"},{"Organ": "organ1", "Tissue": "tissue2"}]',
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},
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])('should format annotation names correctly', ({ obj, expected }) => {
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expect(annotationNamesToGetParams(obj)).toBe(expected);
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});
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});

‎context/app/static/js/api/scfind/types.ts

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interface AnnotationNames {
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Organ: string;
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Tissue: string;
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}
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export type AnnotationNamesList = AnnotationNames[];

‎context/app/static/js/api/scfind/useCellTypeMarkers.ts

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import useSWR from 'swr';
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import { fetcher } from 'js/helpers/swr';
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import { AnnotationNamesList } from './types';
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import { createScfindKey, annotationNamesToGetParams } from './utils';
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interface CellTypeMarkerInfo {
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cellType: string;
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f1: number;
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fn: number;
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fp: number;
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genes: string;
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precision: number;
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recall: number;
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tp: number;
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}
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interface CellTypeMarkersParams {
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cellTypes: string | string[];
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annotationNames: AnnotationNamesList;
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backgroundCellTypes?: string[];
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backgroundAnnotationNames?: AnnotationNamesList;
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topK?: number;
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sortField?: keyof CellTypeMarkerInfo;
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includePrefix?: boolean;
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}
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type CellTypeMarkersKey = string;
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interface CellTypeMarkersResponse {
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cellTypeMarkers: CellTypeMarkerInfo[];
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}
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export function createCellTypeMarkersKey({
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cellTypes,
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annotationNames,
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backgroundCellTypes,
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backgroundAnnotationNames,
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topK,
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sortField,
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includePrefix,
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}: CellTypeMarkersParams): CellTypeMarkersKey {
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return createScfindKey('cellTypeMarkers', {
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cell_types: Array.isArray(cellTypes) ? cellTypes.join(',') : cellTypes,
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annotation_names: annotationNames ? annotationNamesToGetParams(annotationNames) : undefined,
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background_cell_types: Array.isArray(backgroundCellTypes) ? backgroundCellTypes.join(',') : backgroundCellTypes,
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background_annotation_names: annotationNamesToGetParams(backgroundAnnotationNames),
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top_k: topK ? topK.toString() : undefined,
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include_prefix: includePrefix ? String(includePrefix) : undefined,
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sort_field: sortField,
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});
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}
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export default function useCellTypeMarkers({
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topK = 10,
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sortField = 'f1',
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includePrefix = true,
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...params
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}: CellTypeMarkersParams) {
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const key = createCellTypeMarkersKey({ topK, sortField, includePrefix, ...params });
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return useSWR<CellTypeMarkersResponse, unknown, CellTypeMarkersKey>(key, (url) => fetcher({ url }));
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}

‎context/app/static/js/api/scfind/useCellTypeNames.ts

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import useSWR from 'swr';
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import { fetcher } from 'js/helpers/swr';
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import { createScfindKey, annotationNamesToGetParams } from './utils';
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import { AnnotationNamesList } from './types';
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type CellTypeNamesKey = string;
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interface CellTypeNamesParams {
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annotationNames: AnnotationNamesList;
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}
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interface CellTypeNamesResponse {
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cellTypeNames: string[];
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}
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export function createCellTypeNamesKey(annotationNames?: AnnotationNamesList): CellTypeNamesKey {
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return createScfindKey('cellTypeNames', {
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annotation_names: annotationNames ? annotationNamesToGetParams(annotationNames) : undefined,
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});
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}
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export default function useCellTypeNames({ annotationNames }: CellTypeNamesParams) {
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const key = createCellTypeNamesKey(annotationNames);
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return useSWR<CellTypeNamesResponse, unknown, CellTypeNamesKey>(key, (url) => fetcher({ url }));
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}

‎context/app/static/js/api/scfind/useEvaluateMarkers.ts

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import useSWR from 'swr';
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import { fetcher } from 'js/helpers/swr';
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import { createScfindKey, annotationNamesToGetParams } from './utils';
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import { AnnotationNamesList } from './types';
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interface EvaluateMarkersParams {
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geneList: string | string[];
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cellTypes: string | string[];
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annotationNames?: AnnotationNamesList;
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backgroundCellTypes?: string[];
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backgroundAnnotationNames?: AnnotationNamesList;
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sortField?: string;
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includePrefix?: boolean;
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}
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type EvaluateMarkersKey = string;
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interface EvaluateMarkersResponse {
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evaluateMarkers: unknown;
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}
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export function createCellTypeMarkersKey({
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geneList,
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cellTypes,
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annotationNames,
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backgroundCellTypes,
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backgroundAnnotationNames,
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sortField,
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includePrefix,
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}: EvaluateMarkersParams): EvaluateMarkersKey {
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return createScfindKey('evaluateMarkers', {
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gene_list: Array.isArray(geneList) ? geneList.join(',') : geneList,
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cell_types: Array.isArray(cellTypes) ? cellTypes.join(',') : cellTypes,
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annotation_names: annotationNamesToGetParams(annotationNames),
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background_cell_types: Array.isArray(backgroundCellTypes) ? backgroundCellTypes.join(',') : backgroundCellTypes,
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background_annotation_names: annotationNamesToGetParams(backgroundAnnotationNames),
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sort_field: sortField,
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include_prefix: includePrefix !== undefined ? String(includePrefix) : undefined,
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});
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}
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export default function useEvaluateMarkers(params: EvaluateMarkersParams) {
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const key = createCellTypeMarkersKey(params);
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return useSWR<EvaluateMarkersResponse, unknown, EvaluateMarkersKey>(key, (url) => fetcher({ url }));
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}

‎context/app/static/js/api/scfind/useFindCellTypeSpecificities.ts

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import useSWR from 'swr';
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import { fetcher } from 'js/helpers/swr';
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import { createScfindKey, annotationNamesToGetParams } from './utils';
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import { AnnotationNamesList } from './types';
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interface EvaluateMarkersParams {
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geneList?: string | string[];
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annotationNames?: AnnotationNamesList;
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minCells?: number;
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minFraction?: number;
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}
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type EvaluateMarkersKey = string;
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interface EvaluateMarkersResponse {
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evaluateMarkers: unknown;
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}
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export function createCellTypeSpecificitiesKey({
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geneList,
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annotationNames,
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minCells,
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minFraction,
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}: EvaluateMarkersParams): EvaluateMarkersKey {
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return createScfindKey('findCellTypeSpecificities', {
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annotation_names: annotationNamesToGetParams(annotationNames),
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gene_list: Array.isArray(geneList) ? geneList.join(',') : geneList,
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min_cells: minCells ? String(minCells) : undefined,
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min_fraction: minFraction ? String(minFraction) : undefined,
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});
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}
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export default function useFindCellTypeSpecificities(params: EvaluateMarkersParams) {
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const key = createCellTypeSpecificitiesKey(params);
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return useSWR<EvaluateMarkersResponse, unknown, EvaluateMarkersKey>(key, (url) => fetcher({ url }));
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}

‎context/app/static/js/api/scfind/useFindGeneSignatures.ts

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import useSWR from 'swr';
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import { fetcher } from 'js/helpers/swr';
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import { createScfindKey, annotationNamesToGetParams } from './utils';
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import { AnnotationNamesList } from './types';
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interface FindGeneSignaturesParams {
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cellTypes?: string | string[];
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annotationNames?: AnnotationNamesList;
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minCells?: number;
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minFraction?: number;
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}
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type FindGeneSignaturesKey = string;
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interface FindGeneSignaturesResponse {
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evaluateMarkers: unknown;
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}
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export function createFindGeneSignaturesKey({
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cellTypes,
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annotationNames,
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minCells,
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minFraction,
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}: FindGeneSignaturesParams): FindGeneSignaturesKey {
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return createScfindKey('findGeneSignatures', {
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cell_types: Array.isArray(cellTypes) ? cellTypes.join(',') : cellTypes,
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annotation_names: annotationNamesToGetParams(annotationNames),
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min_cells: minCells ? String(minCells) : undefined,
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min_fraction: minFraction ? String(minFraction) : undefined,
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});
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}
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export default function useFindGeneSignatures(params: FindGeneSignaturesParams) {
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const key = createFindGeneSignaturesKey(params);
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return useSWR<FindGeneSignaturesResponse, unknown, FindGeneSignaturesKey>(key, (url) => fetcher({ url }));
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}

‎context/app/static/js/api/scfind/useFindHouseKeepingGenes.ts

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import useSWR from 'swr';
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import { fetcher } from 'js/helpers/swr';
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import { createScfindKey, annotationNamesToGetParams } from './utils';
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import { AnnotationNamesList } from './types';
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interface FindHouseKeepingGenesParams {
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cellTypes?: string | string[];
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annotationNames?: AnnotationNamesList;
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minRecall?: number;
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maxGenes?: number;
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}
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type FindHouseKeepingGenesKey = string;
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interface FindHouseKeepingGenesResponse {
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findHouseKeepingGenes: unknown;
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}
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export function createFindHouseKeepingGenesKey({
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cellTypes,
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annotationNames,
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minRecall,
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maxGenes,
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}: FindHouseKeepingGenesParams): FindHouseKeepingGenesKey {
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return createScfindKey('findHouseKeepingGenes', {
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cell_types: Array.isArray(cellTypes) ? cellTypes.join(',') : cellTypes,
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annotation_names: annotationNamesToGetParams(annotationNames),
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min_recall: minRecall ? String(minRecall) : undefined,
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max_genes: maxGenes ? String(maxGenes) : undefined,
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});
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}
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export default function useFindHouseKeepingGenes(params: FindHouseKeepingGenesParams) {
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const key = createFindHouseKeepingGenesKey(params);
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return useSWR<FindHouseKeepingGenesResponse, unknown, FindHouseKeepingGenesKey>(key, (url) => fetcher({ url }));
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}

‎context/app/static/js/api/scfind/useFindSimilarGenes.ts

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import useSWR from 'swr';
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import { fetcher } from 'js/helpers/swr';
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import { createScfindKey, annotationNamesToGetParams } from './utils';
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import { AnnotationNamesList } from './types';
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interface FindSimilarGenesParams {
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cellTypes?: string | string[];
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annotationNames?: AnnotationNamesList;
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minRecall?: number;
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maxGenes?: number;
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}
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type FindSimilarGenesKey = string;
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interface FindSimilarGenesResponse {
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evaluateMarkers: unknown;
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}
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export function createFindSimilarGenesKey({
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cellTypes,
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annotationNames,
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minRecall,
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maxGenes,
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}: FindSimilarGenesParams): FindSimilarGenesKey {
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return createScfindKey('findSimilarGenes', {
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cell_types: Array.isArray(cellTypes) ? cellTypes.join(',') : cellTypes,
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annotation_names: annotationNamesToGetParams(annotationNames),
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min_recall: minRecall ? String(minRecall) : undefined,
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max_genes: maxGenes ? String(maxGenes) : undefined,
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});
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}
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export default function useFindSimilarGenes(params: FindSimilarGenesParams) {
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const key = createFindSimilarGenesKey(params);
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return useSWR<FindSimilarGenesResponse, unknown, FindSimilarGenesKey>(key, (url) => fetcher({ url }));
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}

‎context/app/static/js/api/scfind/useFindTissueSpecificities.ts

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import useSWR from 'swr';
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import { fetcher } from 'js/helpers/swr';
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import { createScfindKey } from './utils';
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interface FindTissueSpecificitiesParams {
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geneList?: string | string[];
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minCells?: number;
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}
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type FindTissueSpecificitiesKey = string;
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interface FindTissueSpecificitiesResponse {
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evaluateMarkers: unknown;
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}
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export function FindTissueSpecificitiesKey({
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geneList,
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minCells,
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}: FindTissueSpecificitiesParams): FindTissueSpecificitiesKey {
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return createScfindKey('findTissueSpecificities', {
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gene_list: Array.isArray(geneList) ? geneList.join(',') : geneList,
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min_cells: minCells ? String(minCells) : undefined,
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});
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}
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export default function useFindTissueSpecificities(params: FindTissueSpecificitiesParams) {
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const key = FindTissueSpecificitiesKey(params);
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return useSWR<FindTissueSpecificitiesResponse, unknown, FindTissueSpecificitiesKey>(key, (url) => fetcher({ url }));
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}

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