mirror of
https://github.com/chanzuckerberg/cellxgene.git
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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
@@ -0,0 +1,322 @@
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// these TWO statements MUST be first in the file, before any other imports
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import { enableFetchMocks } from "jest-fetch-mock";
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import * as serverMocks from "./serverMocks";
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// OK, continue on!
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import {
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AnnoMatrixLoader,
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clip,
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isubset,
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isubsetMask,
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} from "../../../src/annoMatrix";
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import { Dataframe } from "../../../src/util/dataframe";
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enableFetchMocks();
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describe("AnnoMatrix", () => {
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let annoMatrix;
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beforeEach(async () => {
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fetch.resetMocks(); // reset all fetch mocking state
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annoMatrix = new AnnoMatrixLoader(
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serverMocks.baseDataURL,
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serverMocks.schema.schema
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);
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});
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describe("basics", () => {
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test("annomatrix static checks", () => {
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expect(annoMatrix).toBeDefined();
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expect(annoMatrix.schema).toMatchObject(serverMocks.schema.schema);
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expect(annoMatrix.nObs).toEqual(serverMocks.schema.schema.dataframe.nObs);
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expect(annoMatrix.nVar).toEqual(serverMocks.schema.schema.dataframe.nVar);
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expect(annoMatrix.isView).toBeFalsy();
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expect(annoMatrix.viewOf).toBeUndefined();
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expect(annoMatrix.rowIndex).toBeDefined();
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});
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test("simple single column fetch", async () => {
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fetch.once(serverMocks.annotationsObs(["name_0"]));
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const df = await annoMatrix.fetch("obs", "name_0");
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expect(df).toBeInstanceOf(Dataframe);
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expect(df.colIndex.labels()).toEqual(["name_0"]);
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expect(df.dims).toEqual([annoMatrix.nObs, 1]);
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});
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test("simple multi column fetch", async () => {
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fetch
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.once(serverMocks.annotationsObs(["name_0"]))
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.once(serverMocks.annotationsObs(["n_genes"]));
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await expect(
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annoMatrix.fetch("obs", ["name_0", "n_genes"])
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).resolves.toBeInstanceOf(Dataframe);
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});
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describe("fetch from field", () => {
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const getLastTwo = async (field) => {
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const columnNames = annoMatrix.getMatrixColumns(field).slice(-2);
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fetch.mockResponses(...columnNames.map(() => serverMocks.responder));
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await expect(
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annoMatrix.fetch(field, columnNames)
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).resolves.toBeInstanceOf(Dataframe);
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};
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test("obs", async () => getLastTwo("obs"));
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test("var", async () => getLastTwo("var"));
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test("emb", async () => getLastTwo("emb"));
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});
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test("fetch - test all query forms", async () => {
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// single string is a column name
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fetch.once(serverMocks.annotationsObs(["n_genes"]));
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await expect(annoMatrix.fetch("obs", "n_genes")).resolves.toBeInstanceOf(
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Dataframe
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);
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// array of column names, expecting n_genes to be cached.
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fetch.once(serverMocks.annotationsObs(["percent_mito"]));
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await expect(
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annoMatrix.fetch("obs", ["n_genes", "percent_mito"])
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).resolves.toBeInstanceOf(Dataframe);
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// more complex value filter query, enumerated
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fetch.once(serverMocks.responder);
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await expect(
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annoMatrix.fetch("X", {
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where: {
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field: "var",
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column: annoMatrix.schema.annotations.var.index,
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value: "TYMP",
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},
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})
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).resolves.toBeInstanceOf(Dataframe);
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// more complex value filter query, range
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const varIndex = annoMatrix.schema.annotations.var.index;
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fetch
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.once(
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serverMocks.withExpected("/data/var", [[`var:${varIndex}`, "SUMO3"]])
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)
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.once(
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serverMocks.withExpected("/data/var", [[`var:${varIndex}`, "TYMP"]])
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);
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await expect(
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annoMatrix.fetch("X", [
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{
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where: {
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field: "var",
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column: varIndex,
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value: "SUMO3",
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},
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},
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{
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where: {
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field: "var",
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column: varIndex,
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value: "TYMP",
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},
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},
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])
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).resolves.toBeInstanceOf(Dataframe);
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// XXX inspect the wherecache?
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});
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test("push and pop views", async () => {
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const am1 = clip(annoMatrix, 0.1, 0.9);
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expect(am1.viewOf).toBe(annoMatrix);
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expect(am1.nObs).toEqual(annoMatrix.nObs);
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expect(am1.nVar).toEqual(annoMatrix.nVar);
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expect(am1.rowIndex).toBe(annoMatrix.rowIndex);
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const am2 = clip(annoMatrix, 0.1, 0.9);
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expect(am2.viewOf).toBe(annoMatrix);
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expect(am2).not.toBe(am1);
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expect(am2.rowIndex).toBe(annoMatrix.rowIndex);
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});
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test("schema accessors", () => {
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expect(annoMatrix.getMatrixFields()).toEqual(
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expect.arrayContaining(["X", "obs", "emb", "var"])
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);
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expect(annoMatrix.getMatrixColumns("obs")).toEqual(
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expect.arrayContaining(["name_0", "n_genes", "louvain"])
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);
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expect(annoMatrix.getColumnSchema("emb", "umap")).toEqual({
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name: "umap",
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dims: ["umap_0", "umap_1"],
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type: "float32",
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});
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expect(annoMatrix.getColumnDimensions("emb", "umap")).toEqual([
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"umap_0",
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"umap_1",
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]);
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});
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/*
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test the mask & label access to subset via isubset and isubsetMask
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*/
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test("isubset", async () => {
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const rowList = [0, 10];
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const rowMask = new Uint8Array(annoMatrix.nObs);
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for (let i = 0; i < rowList.length; i += 1) {
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rowMask[rowList[i]] = 1;
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}
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const am1 = isubset(annoMatrix, rowList);
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const am2 = isubsetMask(annoMatrix, rowMask);
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expect(am1).not.toBe(am2);
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expect(am1.nObs).toEqual(2);
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expect(am1.nObs).toEqual(am2.nObs);
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expect(am1.nVar).toEqual(am2.nVar);
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fetch
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.once(serverMocks.annotationsObs(["n_genes"]))
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.once(serverMocks.annotationsObs(["n_genes"]));
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const ng1 = await am1.fetch("obs", "n_genes");
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const ng2 = await am2.fetch("obs", "n_genes");
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expect(ng1).toHaveLength(ng2.length);
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expect(ng1.colIndex.labels()).toEqual(ng2.colIndex.labels());
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expect(ng1.col("n_genes").asArray()).toEqual(
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ng2.col("n_genes").asArray()
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);
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});
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});
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describe("add/drop column", () => {
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async function addDrop(base) {
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expect(base.getMatrixColumns("obs")).not.toContain("foo");
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fetch.mockRejectOnce(new Error("unknown column name"));
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await expect(base.fetch("obs", "foo")).rejects.toThrow(
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"unknown column name"
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);
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/* add */
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const am1 = base.addObsColumn(
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{ name: "foo", type: "float32", writable: true },
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Float32Array,
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0
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);
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expect(base.getMatrixColumns("obs")).not.toContain("foo");
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expect(am1.getMatrixColumns("obs")).toContain("foo");
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const foo = await am1.fetch("obs", "foo");
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expect(foo).toBeDefined();
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expect(foo).toBeInstanceOf(Dataframe);
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expect(foo).toHaveLength(am1.nObs);
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expect(foo.col("foo").asArray()).toEqual(
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new Float32Array(am1.nObs).fill(0)
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);
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/* drop */
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const am2 = am1.dropObsColumn("foo");
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expect(base.getMatrixColumns("obs")).not.toContain("foo");
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expect(am2.getMatrixColumns("obs")).not.toContain("foo");
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fetch.mockRejectOnce(new Error("unknown column name"));
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await expect(am2.fetch("obs", "foo")).rejects.toThrow(
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"unknown column name"
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);
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}
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test("add/drop column, without view", async () => {
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await addDrop(annoMatrix);
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});
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test("add/drop column, with view", async () => {
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const am1 = clip(annoMatrix, 0.1, 0.9);
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await addDrop(am1);
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const am2 = isubset(am1, [0, 1, 2, 20, 30, 400]);
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await addDrop(am2);
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const am3 = isubset(annoMatrix, [10, 0, 7, 3]);
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await addDrop(am3);
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const am4 = clip(am3, 0, 1);
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await addDrop(am4);
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fetch.mockResponse(serverMocks.responder);
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await am1.fetch("obs", am1.getMatrixColumns("obs"));
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await am2.fetch("obs", am2.getMatrixColumns("obs"));
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await am3.fetch("obs", am3.getMatrixColumns("obs"));
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await am4.fetch("obs", am4.getMatrixColumns("obs"));
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fetch.resetMocks();
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await addDrop(am1);
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await addDrop(am2);
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await addDrop(am3);
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await addDrop(am4);
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});
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});
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describe("setObsColumnValues", () => {
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async function addSetDrop(base) {
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/* add column */
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let am = base.addObsColumn(
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{
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name: "test",
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type: "categorical",
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categories: ["unassigned", "red", "green"],
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writable: true,
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},
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Array,
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"unassigned"
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);
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const testVal = await am.fetch("obs", "test");
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expect(testVal.col("test").asArray()).toEqual(
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new Array(am.nObs).fill("unassigned")
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);
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/* set values in column */
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const whichRows = [1, 2, 10];
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const am1 = await am.setObsColumnValues("test", whichRows, "yo");
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const testVal1 = await am1.fetch("obs", "test");
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const expt = new Array(am1.nObs).fill("unassigned");
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for (let i = 0; i < whichRows.length; i += 1) {
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const offset = am1.rowIndex.getOffset(whichRows[i]);
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expt[offset] = "yo";
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}
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expect(testVal1).not.toBe(testVal);
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expect(testVal1.col("test").asArray()).toEqual(expt);
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expect(am1.getColumnSchema("obs", "test").type).toBe("categorical");
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expect(am1.getColumnSchema("obs", "test").categories).toEqual(
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expect.arrayContaining(["unassigned", "red", "green", "yo"])
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);
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/* drop column */
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fetch.mockRejectOnce(new Error("unknown column name"));
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am = am1.dropObsColumn("test");
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await expect(am.fetch("obs", "test")).rejects.toThrow(
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"unknown column name"
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);
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}
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test("set, without a view", async () => {
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await addSetDrop(annoMatrix);
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});
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test("set, with a view", async () => {
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const am1 = clip(annoMatrix, 0.1, 0.9);
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await addSetDrop(am1);
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const am2 = isubset(am1, [0, 1, 2, 10, 20, 30, 400]);
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await addSetDrop(am2);
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const am3 = isubset(annoMatrix, [10, 1, 0, 30, 2]);
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await addSetDrop(am3);
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fetch.mockResponse(serverMocks.responder);
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await am1.fetch("obs", am1.getMatrixColumns("obs"));
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await am2.fetch("obs", am2.getMatrixColumns("obs"));
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await am3.fetch("obs", am3.getMatrixColumns("obs"));
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await addSetDrop(am1);
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await addSetDrop(am2);
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await addSetDrop(am3);
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});
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});
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});
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