mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-10-06 06:18:12 +08:00
Redux refactor (#1571)
* refactor categorical controls state * lint * fix race condition in tests * fix typo * add missing update on subset * remove obsolete code * update jest and puppeteer major version; update all minors * update when label changes * remove lint from tests; increase timeouts in e2e tests * initial refactoring to new async annomatrix * refine error handling * fix bad merge * add continuous legend * lint * fix memoization in color table creators * partial implementation of user defined annotations * add new annotations action creator file * first pass at user annotations * additional user annotation bug fixes * user annotation auto-save * unit test cleanup * lint * refactor into multiple files * cleanup * add column GC * fix several bugs in user annotations * remove debug code * no anonymous functions * undo redo cleanup * file cleanup * scatterplot * performance * cleanup * remove old code * render in parallel with load * fix race condition * simply graph rendering * render throttle DRY * fix category label order * fix typo in e2e test setup * re-fix the e2e test setup * be more tolerant of races * anno matrix unit tests * temp disable reembedding * pilot port continuous histo to react-async * name change * lint * fix repaint bug * typo fix * update snap to match new ids * world/universe name cleanup * move annoMatrix to src dir * use private underscore naming convention * fix corner case in all selected * name cleanup * add layout control * init edge case * lint * port scatterplot * fix label indexing bug and improve tests * port category to react-async * fix user annotation labelling while subset * select all of prev layout on layout switch * fix race with crossfilter update * prettier lint * fix misleading comment * fix url composition in loader * first pass at crossfilter tests * lint * lint * fix typo * improved error handling for network errors * fix memoization bug * add memo * refactor for performnce * add missing single-value handling in select exact parser * small bugs discovered by tests * lint * additional crossfilter unit tests * remove extraneous comment * add support for automatic category determination * lint * fix render bug in category * take advantage of schema categories guarantee * lint * do not clear history when resetting * enhanced annomatrix gc * lint * finish renaming to follow conventions; fix clone race bug * lint * add priority based loading to improve initial data load UX * crossfilter cache perf * perf tuning * remove timers * documentation * PR review changes * PR review changes * more PR review edits * improve clarity of comment * more PR review fixes * port centroidLabels to use react-async * remove dead code * pr review updates * oops, remove logging
This commit is contained in:
Bruce Martin
@@ -0,0 +1,11 @@
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export const baseDataURL = "https://a.fake.url/api/v0.2";
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window.CELLXGENE = {
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API: {
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prefix: baseDataURL,
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version: "v0.2/",
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},
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};
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export { schema } from "./schema";
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export * from "./routes";
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@@ -0,0 +1,211 @@
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import { schema } from "./schema";
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import { Dataframe, KeyIndex } from "../../../../src/util/dataframe";
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import { encodeMatrixFBS } from "../../../../src/util/stateManager/matrix";
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const indexedSchema = {
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obsByName: Object.fromEntries(
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schema.schema.annotations.obs.columns.map((v) => [v.name, v]) ?? []
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),
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varByName: Object.fromEntries(
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schema.schema.annotations.var.columns.map((v) => [v.name, v]) ?? []
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),
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embByName: Object.fromEntries(
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schema.schema.layout.obs.map((v) => [v.name, v]) ?? []
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),
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};
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function makeMockColumn(s, length) {
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const { type } = s;
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switch (type) {
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case "int32":
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return new Int32Array(length).fill(Math.floor(99 * Math.random()));
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case "string":
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return new Array(length).fill("test");
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case "float32":
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return new Float32Array(length).fill(99 * Math.random());
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case "boolean":
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return new Array(length).fill(false);
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case "categorical":
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return new Array(length).fill(s.categories[0]);
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default:
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throw new Error("unkonwn type");
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}
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}
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function getEncodedDataframe(colNames, length, colSchemas) {
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const colIndex = new KeyIndex(colNames);
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const columns = colSchemas.map((s) => makeMockColumn(s, length));
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const df = new Dataframe([length, colNames.length], columns, null, colIndex);
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const body = encodeMatrixFBS(df);
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return body;
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}
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export function dataframeResponse(colNames, columns) {
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const colIndex = new KeyIndex(colNames);
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const df = new Dataframe(
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[columns[0].length, colNames.length],
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columns,
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null,
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colIndex
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);
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const body = encodeMatrixFBS(df);
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const headers = new Headers({
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"Content-Type": "application/octet-stream",
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});
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return () => Promise.resolve({ body, init: { status: 200, headers } });
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}
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function annotationObsResponse(request) {
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const url = new URL(request.url);
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const params = Array.from(url.searchParams.entries());
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const names = params
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.filter(([k]) => k === "annotation-name")
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.map(([, v]) => v);
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if (!names.every((n) => indexedSchema.obsByName[n])) {
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return Promise.reject(new Error("bad obs annotation name in URL"));
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}
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const colSchemas = names.map((n) => indexedSchema.obsByName[n]);
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const body = getEncodedDataframe(
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names,
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schema.schema.dataframe.nObs,
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colSchemas
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);
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const headers = new Headers({
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"Content-Type": "application/octet-stream",
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});
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return Promise.resolve({
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body,
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init: { status: 200, headers },
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});
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}
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function annotationVarResponse(request) {
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const url = new URL(request.url);
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const params = Array.from(url.searchParams.entries());
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const names = params
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.filter(([k]) => k === "annotation-name")
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.map(([, v]) => v);
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if (!names.every((n) => indexedSchema.varByName[n])) {
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return Promise.reject(new Error("bad var annotation name in URL"));
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}
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const colSchemas = names.map((n) => indexedSchema.varByName[n]);
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const body = getEncodedDataframe(
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names,
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schema.schema.dataframe.nVar,
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colSchemas
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);
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const headers = new Headers({
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"Content-Type": "application/octet-stream",
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});
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return Promise.resolve({
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body,
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init: { status: 200, headers },
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});
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}
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function layoutObsResponse(request) {
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const url = new URL(request.url);
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const params = Array.from(url.searchParams.entries());
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const names = params.filter(([k]) => k === "layout-name").map(([, v]) => v);
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if (!names.every((n) => indexedSchema.embByName[n])) {
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return Promise.reject(new Error("bad layout name in URL"));
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}
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const dims = names.map((n) => indexedSchema.embByName[n].dims).flat();
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const colSchemas = names
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.map((n) => [indexedSchema.embByName[n], indexedSchema.embByName[n]])
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.flat();
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const body = getEncodedDataframe(
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dims,
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schema.schema.dataframe.nObs,
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colSchemas
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);
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const headers = new Headers({
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"Content-Type": "application/octet-stream",
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});
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return Promise.resolve({
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body,
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init: { status: 200, headers },
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});
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}
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function dataVarResponse(request) {
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const url = new URL(request.url);
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const params = Array.from(url.searchParams.entries());
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const colNames = params.map((v) => `${v[0]}/${v[1]}`);
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const colSchemas = colNames.map(() => schema.schema.dataframe);
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const body = getEncodedDataframe(
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colNames,
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schema.schema.dataframe.nObs,
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colSchemas
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);
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const headers = new Headers({
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"Content-Type": "application/octet-stream",
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});
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return Promise.resolve({
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body,
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init: { status: 200, headers },
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});
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}
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export function responder(request) {
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const url = new URL(request.url);
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const { pathname } = url;
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if (pathname.endsWith("/annotations/obs")) {
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return annotationObsResponse(request);
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}
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if (pathname.endsWith("/annotations/var")) {
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return annotationVarResponse(request);
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}
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if (pathname.endsWith("/layout/obs")) {
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return layoutObsResponse(request);
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}
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if (pathname.endsWith("/data/var")) {
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return dataVarResponse(request);
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}
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return Promise.reject(new Error("bad URL"));
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}
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export function withExpected(expectedURL, expectedParams) {
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/*
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Do some additional error checking
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*/
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return (request) => {
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// if URL is bogus, reject the promise
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const url = new URL(request.url);
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if (!url.pathname.endsWith(expectedURL)) {
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return Promise.reject(new Error("Unexpected URL!"));
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}
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const params = Array.from(url.searchParams.entries()).sort(
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(a, b) => a[0] < b[0]
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);
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expectedParams = expectedParams.slice().sort((a, b) => a[0] < b[0]);
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if (
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params.length !== expectedParams.length ||
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!params.every(
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(p, i) => p[0] === expectedParams[i][0] && p[1] === expectedParams[i][1]
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)
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) {
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return Promise.reject(new Error("unexpected name requested in URL"));
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}
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return responder(request);
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};
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}
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export function annotationsObs(names) {
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return withExpected(
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"/annotations/obs",
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names.map((name) => ["annotation-name", name])
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);
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}
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@@ -0,0 +1,80 @@
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export const schema = {
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schema: {
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annotations: {
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obs: {
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columns: [
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{
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name: "name_0",
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type: "string",
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writable: false,
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},
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{
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name: "n_genes",
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type: "int32",
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writable: false,
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},
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{
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name: "percent_mito",
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type: "float32",
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writable: false,
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},
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{
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name: "n_counts",
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type: "float32",
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writable: false,
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},
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{
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name: "louvain",
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type: "string",
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writable: false,
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},
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],
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index: "name_0",
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},
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var: {
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columns: [
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{
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name: "name_0",
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type: "string",
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writable: false,
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},
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{
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name: "n_cells",
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type: "int32",
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writable: false,
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},
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],
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index: "name_0",
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},
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},
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dataframe: {
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nObs: 2638,
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nVar: 1838,
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type: "float32",
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},
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layout: {
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obs: [
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{
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dims: ["draw_graph_fr_0", "draw_graph_fr_1"],
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name: "draw_graph_fr",
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type: "float32",
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},
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{
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dims: ["pca_0", "pca_1"],
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name: "pca",
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type: "float32",
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},
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{
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dims: ["tsne_0", "tsne_1"],
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name: "tsne",
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type: "float32",
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},
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{
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dims: ["umap_0", "umap_1"],
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name: "umap",
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type: "float32",
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},
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],
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},
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},
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};
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