mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-10-06 07:28:12 +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
@@ -1,90 +0,0 @@
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import * as Universe from "../../../src/util/stateManager/universe";
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import { matrixFBSToDataframe } from "../../../src/util/stateManager/matrix";
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import * as Dataframe from "../../../src/util/dataframe";
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import * as REST from "./sampleResponses";
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describe("createUniverseFromResponse", () => {
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/*
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test createUniverseFromResponse - this function converts
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a set of REST 0.2 responses into a "new" Universe.
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createUniverseFromResponse(
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configResponse,
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schemaResponse,
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annotationsObsResponse,
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annotationsVarResponse,
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layoutObsResponse
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) --> Universe
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where:
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configResponse: GET /.../config
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schemaResponse: GET /.../schema
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annotationsObsResponse: GET /.../annotations/obs
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annotationsVarResponse: GET /.../annotations/var
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layoutObsResponse: GET /.../layout/obs
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See spec in docs/REST_API.md.
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*/
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test("create from test data", () => {
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/*
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create a universe from sample data nad validate its shape & contents
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*/
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const { nObs, nVar } = REST.schema.schema.dataframe;
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let universe = Universe.createUniverseFromResponse(
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REST.config,
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REST.schema
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);
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expect(universe).toBeDefined();
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expect(universe).toMatchObject(
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expect.objectContaining({
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nObs,
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nVar,
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schema: REST.schema.schema,
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obsAnnotations: expect.any(Dataframe.Dataframe),
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varAnnotations: expect.any(Dataframe.Dataframe),
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obsLayout: expect.any(Dataframe.Dataframe),
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varData: expect.any(Dataframe.Dataframe),
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})
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);
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universe = {
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...universe,
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...Universe.addObsAnnotations(
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universe,
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matrixFBSToDataframe(REST.annotationsObs)
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),
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...Universe.addVarAnnotations(
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universe,
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matrixFBSToDataframe(REST.annotationsVar)
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),
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...Universe.addObsLayout(universe, matrixFBSToDataframe(REST.layoutObs)),
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};
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expect(universe).toMatchObject(
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expect.objectContaining({
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nObs,
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nVar,
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schema: REST.schema.schema,
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obsAnnotations: expect.any(Dataframe.Dataframe),
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varAnnotations: expect.any(Dataframe.Dataframe),
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obsLayout: expect.any(Dataframe.Dataframe),
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varData: expect.any(Dataframe.Dataframe),
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})
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);
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expect(universe.obsAnnotations.dims).toEqual([
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nObs,
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REST.schema.schema.annotations.obs.columns.length,
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]);
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expect(universe.obsLayout.dims).toEqual([nObs, 2]);
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expect(universe.obsLayout.colIndex.labels()).toEqual(
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universe.schema.layout.obs[0].dims
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);
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expect(universe.varAnnotations.dims).toEqual([
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nVar,
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REST.schema.schema.annotations.var.columns.length,
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]);
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expect(universe.varData.isEmpty()).toBeTruthy();
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});
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});
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@@ -1,202 +0,0 @@
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import _ from "lodash";
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import * as Universe from "../../../src/util/stateManager/universe";
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import { matrixFBSToDataframe } from "../../../src/util/stateManager/matrix";
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import * as World from "../../../src/util/stateManager/world";
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import * as Dataframe from "../../../src/util/dataframe";
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import Crossfilter from "../../../src/util/typedCrossfilter";
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import { DimTypes } from "../../../src/util/typedCrossfilter/crossfilter";
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import * as REST from "./sampleResponses";
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import {
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obsAnnoDimensionName,
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layoutDimensionName,
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} from "../../../src/util/nameCreators";
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/*
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Helper - creates universe, world, corssfilter and dimensionMap from
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the default REST test response.
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*/
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const defaultBigBang = () => {
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/* create unverse, world, crossfilter and dimensionMap */
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/* create universe */
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let universe = Universe.createUniverseFromResponse(
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_.cloneDeep(REST.config),
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_.cloneDeep(REST.schema)
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);
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universe = {
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...universe,
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...Universe.addObsAnnotations(
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universe,
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matrixFBSToDataframe(REST.annotationsObs)
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),
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...Universe.addVarAnnotations(
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universe,
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matrixFBSToDataframe(REST.annotationsVar)
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),
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...Universe.addObsLayout(universe, matrixFBSToDataframe(REST.layoutObs)),
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};
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/* create world */
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const world = World.createWorldFromEntireUniverse(universe);
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/* create crossfilter */
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const crossfilter = World.createObsDimensions(
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new Crossfilter(world.obsAnnotations),
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world,
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REST.schema.schema.layout.obs[0].dims
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);
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return {
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universe,
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world,
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crossfilter,
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};
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};
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describe("createWorldFromEntireUniverse", () => {
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test("create from REST sample", () => {
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const universe = Universe.createUniverseFromResponse(
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_.cloneDeep(REST.config),
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_.cloneDeep(REST.schema),
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matrixFBSToDataframe(_.cloneDeep(REST.annotationsObs)),
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matrixFBSToDataframe(_.cloneDeep(REST.annotationsVar)),
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matrixFBSToDataframe(_.cloneDeep(REST.layoutObs))
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);
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expect(universe).toBeDefined();
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const world = World.createWorldFromEntireUniverse(universe);
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expect(world).toBeDefined();
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expect(world).toMatchObject(
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expect.objectContaining({
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nObs: universe.nObs,
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nVar: universe.nVar,
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schema: universe.schema,
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obsAnnotations: expect.any(Dataframe.Dataframe),
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varAnnotations: expect.any(Dataframe.Dataframe),
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obsLayout: expect.any(Dataframe.Dataframe),
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varData: expect.any(Dataframe.Dataframe),
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clipQuantiles: { min: 0, max: 1 },
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unclipped: {
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obsAnnotations: expect.any(Dataframe.Dataframe),
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varData: expect.any(Dataframe.Dataframe),
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},
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})
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);
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});
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});
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describe("createWorldFromCurrentSelection", () => {
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test("create from REST sample", () => {
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const {
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universe,
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world: originalWorld,
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crossfilter: originalCrossfilter,
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} = defaultBigBang();
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/* mock a selection */
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const crossfilter = originalCrossfilter
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.select(obsAnnoDimensionName("field1"), { mode: "range", lo: 0, hi: 5 })
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.select(obsAnnoDimensionName("field3"), {
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mode: "exact",
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values: [false],
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});
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/* create the world from the selection */
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const world = World.createWorldBySelection(
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universe,
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originalWorld,
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crossfilter
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);
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expect(world).toBeDefined();
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expect(world.nObs).toEqual(crossfilter.countSelected());
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/*
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calculate expected values and match against result
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*/
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/* matchFilter must match the dimension filters above */
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const matchFilter = (df, row) => {
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const field1 = df.at(row, "field1");
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const field3 = df.at(row, "field3");
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return field1 >= 0 && field1 < 5 && !field3;
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};
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const matchingIndices = _()
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.range(universe.nObs)
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.filter((idx) => matchFilter(universe.obsAnnotations, idx))
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.value();
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expect(world).toMatchObject(
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expect.objectContaining({
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nObs: matchingIndices.length,
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nVar: universe.nVar,
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schema: universe.schema,
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clipQuantiles: { min: 0, max: 1 },
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obsAnnotations: expect.any(Dataframe.Dataframe),
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varAnnotations: expect.any(Dataframe.Dataframe),
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obsLayout: expect.any(Dataframe.Dataframe),
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varData: expect.any(Dataframe.Dataframe),
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unclipped: {
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obsAnnotations: expect.any(Dataframe.Dataframe),
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varData: expect.any(Dataframe.Dataframe),
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},
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})
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);
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expect(world.obsAnnotations.rowIndex.labels()).toEqual(
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new Int32Array(matchingIndices)
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);
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expect(world.obsAnnotations.colIndex.labels()).toEqual(
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universe.obsAnnotations.colIndex.labels()
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);
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expect(world.obsLayout.rowIndex.labels()).toEqual(
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new Int32Array(matchingIndices)
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);
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expect(world.obsLayout.colIndex.labels()).toEqual(
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world.schema.layout.obs[0].dims
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);
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});
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});
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describe("createObsDimensionMap", () => {
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test("when universe eq world", () => {
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/*
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check for:
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- creates a dimension for all obsAnnotations, PLUS X/Y layout
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- check that dimension typing is sane
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*/
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const { crossfilter } = defaultBigBang();
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const annotationNames = _.map(
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REST.schema.schema.annotations.obs.columns,
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(c) => c.name
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);
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const obsIndexColName = REST.schema.schema.annotations.obs.index;
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const schemaByObsName = _.keyBy(
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REST.schema.schema.annotations.obs.columns,
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"name"
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);
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expect(crossfilter).toBeDefined();
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annotationNames.forEach((name) => {
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const dim = crossfilter.dimensions[obsAnnoDimensionName(name)];
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if (name === obsIndexColName) {
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expect(dim).toBeUndefined();
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} else {
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const { type } = schemaByObsName[name];
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if (type === "string" || type === "boolean" || type === "categorical") {
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expect(dim.dim).toBeInstanceOf(DimTypes.enum);
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} else {
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expect(dim.dim).toBeInstanceOf(DimTypes.scalar);
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}
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}
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});
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expect(
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crossfilter.dimensions[layoutDimensionName("XY")].dim
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).toBeInstanceOf(DimTypes.spatial);
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});
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});
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describe("worldEqUniverse", () => {
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const { universe, world } = defaultBigBang();
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const result = World.worldEqUniverse(world, universe);
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expect(result).toBe(true);
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});
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