mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-30 09:18:11 +08:00
TS Revert (1) (#2402)
* revert all commits to before Typescript migration * update compat workflow to match latest deps (#2335) * update compat workflow to match latest deps * attempt to debug * attempt to debug * remove debugging code * typo * update deps to match desktop (#2340) * fix: don't run lint with `--fix` on push tests (#2273) * fix: don't run lint with `--fix` on push tests * npx Co-authored-by: maniarathi <mani.arathi@gmail.com> Co-authored-by: Madison Dunitz <madison.dunitz@chanzuckerberg.com> * rename X_approx_distribution to X_approximate_distribution (#2337) * Correctly handle non-finite numbers in heuristic determination of X distribution (#2342) * handle non-finites explicitly * improve and test edge case handling for distribution estimation * revert debugging changes * code readability * clean up type inferencing (#2332) * unit tests for 64 bit conversion * clean up type handling * type inference tests * more type inference fixes * use schema to determine user intent for data typing * stop using deprecated API * fbs type encoding test * add missing test * add more tests * correctly infer X type for CXG adaptor * lint * fix typo * ts migration * cleanup from PR review * lint * PR review changes * remove unused packages from client (#2359) * remove unused packages from client * add missing peer dep * fix: disable FE auth testing on compatibility tests (#2377) * update: release process (#2277) Co-authored-by: maniarathi <mani.arathi@gmail.com> * fix: remove spaces in param setup (#2380) * delete deploy workflow (#2396) * undo reformatting which now does not pass lint * fix snapshots which changed due to npm dep changes * add missing quoting to snapshot * another snapshot typo fix * TS Revert (2) - replay PR #2347 and #2354 (#2403) * replay edits from PR 2347 * TS Revert (3) - replay edits in PR #2327 (#2404) * replay edits in PR 2327 * TS Revert (4) - replay PR #2355 (#2405) * replay edits in PR 2355 * add additional babel config * reformat with new prettier config Co-authored-by: Severiano Badajoz <sbadajoz@chanzuckerberg.com> Co-authored-by: maniarathi <mani.arathi@gmail.com> Co-authored-by: Madison Dunitz <madison.dunitz@chanzuckerberg.com>
This commit is contained in:
Bruce Martin
co-authored by
maniarathi
Madison Dunitz
Severiano Badajoz
maniarathi
Madison Dunitz
Severiano Badajoz
parent
295590a7c6
commit
eaae6df5e3
+1
-2
@@ -1,7 +1,6 @@
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export const baseDataURL = "https://a.fake.url/api/v0.2";
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// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
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(window as any).CELLXGENE = {
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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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@@ -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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@@ -1,249 +0,0 @@
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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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// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
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function makeMockColumn(s: any, length: any) {
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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("unknown type");
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}
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}
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// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
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function getEncodedDataframe(colNames: any, length: any, colSchemas: any) {
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const colIndex = new KeyIndex(colNames);
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// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
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const columns = colSchemas.map((s: any) => 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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// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
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export function dataframeResponse(colNames: any, columns: any) {
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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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// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
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function annotationObsResponse(request: any) {
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const url = new URL(request.url);
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// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
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const params = Array.from((url.searchParams as any).entries());
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const names = params
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// @ts-expect-error ts-migrate(2769) FIXME: No overload matches this call.
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.filter(([k]) => k === "annotation-name")
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// @ts-expect-error ts-migrate(2345) FIXME: Argument of type '([, v]: [any, any]) => any' is n... Remove this comment to see the full error message
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.map(([, v]) => v);
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// @ts-expect-error ts-migrate(2538) FIXME: Type 'unknown' cannot be used as an index type.
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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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// @ts-expect-error ts-migrate(2538) FIXME: Type 'unknown' cannot be used as an index type.
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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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// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
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function annotationVarResponse(request: any) {
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const url = new URL(request.url);
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// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
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const params = Array.from((url.searchParams as any).entries());
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const names = params
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// @ts-expect-error ts-migrate(2769) FIXME: No overload matches this call.
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.filter(([k]) => k === "annotation-name")
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// @ts-expect-error ts-migrate(2345) FIXME: Argument of type '([, v]: [any, any]) => any' is n... Remove this comment to see the full error message
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.map(([, v]) => v);
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// @ts-expect-error ts-migrate(2538) FIXME: Type 'unknown' cannot be used as an index type.
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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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// @ts-expect-error ts-migrate(2538) FIXME: Type 'unknown' cannot be used as an index type.
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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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// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
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function layoutObsResponse(request: any) {
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const url = new URL(request.url);
|
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// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
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const params = Array.from((url.searchParams as any).entries());
|
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// @ts-expect-error ts-migrate(2769) FIXME: No overload matches this call.
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const names = params.filter(([k]) => k === "layout-name").map(([, v]) => v);
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// @ts-expect-error ts-migrate(2538) FIXME: Type 'unknown' cannot be used as an index type.
|
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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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// @ts-expect-error ts-migrate(2538) FIXME: Type 'unknown' cannot be used as an index type.
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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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// @ts-expect-error ts-migrate(2538) FIXME: Type 'unknown' cannot be used as an index type.
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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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|
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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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|
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// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
|
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function dataVarResponse(request: any) {
|
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const url = new URL(request.url);
|
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// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
|
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const params = Array.from((url.searchParams as any).entries());
|
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|
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// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
|
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const colNames = params.map((v) => `${(v as any)[0]}/${(v as any)[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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);
|
||||
|
||||
const headers = new Headers({
|
||||
"Content-Type": "application/octet-stream",
|
||||
});
|
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return Promise.resolve({
|
||||
body,
|
||||
init: { status: 200, headers },
|
||||
});
|
||||
}
|
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|
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// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
|
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export function responder(request: any) {
|
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const url = new URL(request.url);
|
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const { pathname } = url;
|
||||
if (pathname.endsWith("/annotations/obs")) {
|
||||
return annotationObsResponse(request);
|
||||
}
|
||||
if (pathname.endsWith("/annotations/var")) {
|
||||
return annotationVarResponse(request);
|
||||
}
|
||||
if (pathname.endsWith("/layout/obs")) {
|
||||
return layoutObsResponse(request);
|
||||
}
|
||||
if (pathname.endsWith("/data/var")) {
|
||||
return dataVarResponse(request);
|
||||
}
|
||||
return Promise.reject(new Error("bad URL"));
|
||||
}
|
||||
|
||||
// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
|
||||
export function withExpected(expectedURL: any, expectedParams: any) {
|
||||
/*
|
||||
Do some additional error checking
|
||||
*/
|
||||
// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
|
||||
return (request: any) => {
|
||||
// if URL is bogus, reject the promise
|
||||
const url = new URL(request.url);
|
||||
if (!url.pathname.endsWith(expectedURL)) {
|
||||
return Promise.reject(new Error("Unexpected URL!"));
|
||||
}
|
||||
// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
|
||||
const params = Array.from((url.searchParams as any).entries()).sort(
|
||||
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type '(a: unknown, b: unknown) => bool... Remove this comment to see the full error message
|
||||
// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
|
||||
(a, b) => (a as any)[0] < (b as any)[0]
|
||||
);
|
||||
expectedParams = expectedParams
|
||||
.slice() // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
|
||||
.sort((a: any, b: any) => a[0] < b[0]);
|
||||
|
||||
if (
|
||||
params.length !== expectedParams.length ||
|
||||
!params.every(
|
||||
(p, i) =>
|
||||
// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
|
||||
(p as any)[0] === expectedParams[i][0] && // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
|
||||
(p as any)[1] === expectedParams[i][1]
|
||||
)
|
||||
) {
|
||||
return Promise.reject(new Error("unexpected name requested in URL"));
|
||||
}
|
||||
|
||||
return responder(request);
|
||||
};
|
||||
}
|
||||
|
||||
// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
|
||||
export function annotationsObs(names: any) {
|
||||
return withExpected(
|
||||
"/annotations/obs",
|
||||
// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
|
||||
names.map((name: any) => ["annotation-name", name])
|
||||
);
|
||||
}
|
||||
+1
-3
@@ -1,6 +1,4 @@
|
||||
import { RawSchema } from "../../../../src/common/types/schema";
|
||||
|
||||
export const schema: { schema: RawSchema } = {
|
||||
export const schema = {
|
||||
schema: {
|
||||
annotations: {
|
||||
obs: {
|
||||
Reference in New Issue
Block a user