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

client/__tests__/util/centroid.test.js

@@ -1,40 +1,36 @@
 import _ from "lodash";
 
 import calcCentroid from "../../src/util/centroid";
-
 import quantile from "../../src/util/quantile";
-import * as Universe from "../../src/util/stateManager/universe";
 import { matrixFBSToDataframe } from "../../src/util/stateManager/matrix";
-import * as World from "../../src/util/stateManager/world";
 import * as REST from "./stateManager/sampleResponses";
+import { indexEntireSchema } from "../../src/util/stateManager/schemaHelpers";
+import { _normalizeCategoricalSchema } from "../../src/annoMatrix/schema";
 
 describe("centroid", () => {
-  let world;
+  let schema;
+  let obsAnnotations;
+  let obsLayout;
 
   beforeAll(() => {
-    // Create world + universe
-    let universe = Universe.createUniverseFromResponse(
-      _.cloneDeep(REST.config),
-      _.cloneDeep(REST.schema)
-    );
+    schema = indexEntireSchema(_.cloneDeep(REST.schema.schema));
+    obsAnnotations = matrixFBSToDataframe(REST.annotationsObs);
+    obsLayout = matrixFBSToDataframe(REST.layoutObs);
 
-    universe = {
-      ...universe,
-      ...Universe.addObsAnnotations(
-        universe,
-        matrixFBSToDataframe(REST.annotationsObs)
-      ),
-      ...Universe.addVarAnnotations(
-        universe,
-        matrixFBSToDataframe(REST.annotationsVar)
-      ),
-      ...Universe.addObsLayout(universe, matrixFBSToDataframe(REST.layoutObs)),
-    };
-    world = World.createWorldFromEntireUniverse(universe);
+    _normalizeCategoricalSchema(
+      schema.annotations.obsByName.field3,
+      obsAnnotations.col("field3")
+    );
   });
 
   test("field4 (categorical obsAnnotation)", () => {
-    const centroidResult = calcCentroid(world, "field4", ["umap_0", "umap_1"]);
+    const centroidResult = calcCentroid(
+      schema,
+      "field4",
+      obsAnnotations,
+      { current: "umap", currentDimNames: ["umap_0", "umap_1"] },
+      obsLayout
+    );
 
     // Check to see that a centroid has been calculated for every categorical value
     const keysAsArray = Array.from(centroidResult.keys());
@@ -44,8 +40,8 @@ describe("centroid", () => {
 
     // This expected result assumes that all cells belong in all categorical values inside of sample response
     const expectedResult = [
-      quantile([0.5], world.obsLayout.col("umap_0").asArray())[0],
-      quantile([0.5], world.obsLayout.col("umap_1").asArray())[0],
+      quantile([0.5], obsLayout.col("umap_0").asArray())[0],
+      quantile([0.5], obsLayout.col("umap_1").asArray())[0],
     ];
 
     centroidResult.forEach((coordinate) => {
@@ -54,7 +50,13 @@ describe("centroid", () => {
   });
 
   test("field3 (boolean obsAnnotation)", () => {
-    const centroidResult = calcCentroid(world, "field3", ["umap_0", "umap_1"]);
+    const centroidResult = calcCentroid(
+      schema,
+      "field3",
+      obsAnnotations,
+      { current: "umap", currentDimNames: ["umap_0", "umap_1"] },
+      obsLayout
+    );
 
     // Check to see that a centroid has been calculated for every categorical value
     const keysAsArray = Array.from(centroidResult.keys());
@@ -62,8 +64,8 @@ describe("centroid", () => {
 
     // This expected result assumes that all cells belong in all categorical values inside of sample response
     const expectedResult = [
-      quantile([0.5], world.obsLayout.col("umap_0").asArray())[0],
-      quantile([0.5], world.obsLayout.col("umap_1").asArray())[0],
+      quantile([0.5], obsLayout.col("umap_0").asArray())[0],
+      quantile([0.5], obsLayout.col("umap_1").asArray())[0],
     ];
 
     centroidResult.forEach((coordinate) => {