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/src/components/menubar/cellSetButtons.js

@@ -2,7 +2,6 @@
 import React from "react";
 import { AnchorButton, Tooltip } from "@blueprintjs/core";
 import { connect } from "react-redux";
-import { World } from "../../util/stateManager";
 import { tooltipHoverOpenDelay } from "../../globals";
 
 @connect()
@@ -15,12 +14,8 @@ class CellSetButton extends React.PureComponent {
       eitherCellSetOneOrTwo,
     } = this.props;
 
-    // Reducer and components assume that value will be null if
-    // no selection made.  World..getSelectedByIndex() returns a
-    // zero length TypedArray when nothing is selected.
-    let set = World.getSelectedByIndex(crossfilter);
+    let set = crossfilter.allSelectedLabels();
     if (set.length === 0) set = null;
-
     if (!differential.diffExp) {
       /* diffexp needs to be cleared before we store a new set */
       dispatch({

client/src/components/menubar/diffexpButtons.js

@@ -9,7 +9,7 @@ import CellSetButton from "./cellSetButtons";
 
 @connect((state) => ({
   config: state.config,
-  crossfilter: state.crossfilter,
+  crossfilter: state.obsCrossfilter,
   differential: state.differential,
   celllist1: state.differential?.celllist1,
   celllist2: state.differential?.celllist2,

client/src/components/menubar/embedding.js

@@ -1,6 +1,5 @@
 import React from "react";
 import {
-  AnchorButton,
   ButtonGroup,
   Popover,
   Button,
@@ -12,26 +11,25 @@ import {
 import { connect } from "react-redux";
 import * as globals from "../../globals";
 import styles from "./menubar.css";
-import { World } from "../../util/stateManager";
 import actions from "../../actions";
 
 @connect((state) => ({
-  universe: state.universe,
-  world: state.world,
   layoutChoice: state.layoutChoice,
-  reembedController: state.reembedController,
-  enableReembedding: state.config?.parameters?.["enable-reembedding"] ?? false,
+  // disabled temporarily. TODO - issue #1606
+  // reembedController: state.reembedController,
+  // enableReembedding: state.config?.parameters?.["enable-reembedding"] ?? false,
+  enableReembedding: false,
 }))
 class Embedding extends React.PureComponent {
   handleLayoutChoiceChange = (e) => {
     const { dispatch } = this.props;
-    dispatch({
-      type: "set layout choice",
-      layoutChoice: e.currentTarget.value,
-    });
+    dispatch(actions.layoutChoiceAction(e.currentTarget.value));
   };
 
+  // eslint-disable-next-line class-methods-use-this -- temporary disable
   renderReembedding() {
+    return null;
+    /* disabled pending rewrite. TODO - issue #1606
     const {
       enableReembedding,
       world,
@@ -63,6 +61,7 @@ class Embedding extends React.PureComponent {
         />
       </Tooltip>
     );
+*/
   }
 
   render() {

client/src/components/menubar/index.js

@@ -1,4 +1,3 @@
-// jshint esversion: 6
 import React from "react";
 import { connect } from "react-redux";
 import { ButtonGroup, AnchorButton, Tooltip } from "@blueprintjs/core";
@@ -14,13 +13,12 @@ import UndoRedoReset from "./undoRedo";
 import DiffexpButtons from "./diffexpButtons";
 
 @connect((state) => ({
-  universe: state.universe,
-  world: state.world,
-  crossfilter: state.crossfilter,
+  annoMatrix: state.annoMatrix,
+  crossfilter: state.obsCrossfilter,
   differential: state.differential,
   graphInteractionMode: state.controls.graphInteractionMode,
-  clipPercentileMin: Math.round(100 * (state.world?.clipQuantiles?.min ?? 0)),
-  clipPercentileMax: Math.round(100 * (state.world?.clipQuantiles?.max ?? 1)),
+  clipPercentileMin: Math.round(100 * (state.annoMatrix?.clipRange?.[0] ?? 0)),
+  clipPercentileMax: Math.round(100 * (state.annoMatrix?.clipRange?.[1] ?? 1)),
   userDefinedGenes: state.controls.userDefinedGenes,
   diffexpGenes: state.controls.diffexpGenes,
   colorAccessor: state.colors.colorAccessor,
@@ -78,10 +76,10 @@ class MenuBar extends React.Component {
     const { pendingClipPercentiles } = this.state;
     const clipPercentileMin = pendingClipPercentiles?.clipPercentileMin;
     const clipPercentileMax = pendingClipPercentiles?.clipPercentileMax;
-
-    const { world } = this.props;
-    const currentClipMin = 100 * world?.clipQuantiles?.min;
-    const currentClipMax = 100 * world?.clipQuantiles?.max;
+    const {
+      clipPercentileMin: currentClipMin,
+      clipPercentileMax: currentClipMax,
+    } = this.props;
 
     // if you change this test, be careful with logic around
     // comparisons between undefined / NaN handling.
@@ -150,10 +148,7 @@ class MenuBar extends React.Component {
     const { clipPercentileMin, clipPercentileMax } = pendingClipPercentiles;
     const min = clipPercentileMin / 100;
     const max = clipPercentileMax / 100;
-    dispatch({
-      type: "set clip quantiles",
-      clipQuantiles: { min, max },
-    });
+    dispatch(actions.clipAction(min, max));
   };
 
   handleClipOpening = () => {
@@ -178,15 +173,15 @@ class MenuBar extends React.Component {
 
   subsetPossible = () => {
     const { crossfilter } = this.props;
+    const count = crossfilter.countSelected();
     return (
-      crossfilter.countSelected() !== 0 &&
-      crossfilter.countSelected() !== crossfilter.size()
+      count !== 0 && count !== crossfilter.size() // ie, not all are selected
     );
   };
 
   subsetResetPossible = () => {
-    const { world, universe } = this.props;
-    return world.nObs !== universe.nObs;
+    const { annoMatrix } = this.props;
+    return annoMatrix.nObs !== annoMatrix.schema.dataframe.nObs;
   };
 
   render() {
@@ -317,12 +312,10 @@ class MenuBar extends React.Component {
           subsetPossible={this.subsetPossible()}
           subsetResetPossible={this.subsetResetPossible()}
           handleSubset={() => {
-            dispatch(actions.setWorldToSelection());
-            dispatch({ type: "increment graph render counter" });
+            dispatch(actions.subsetAction());
           }}
           handleSubsetReset={() => {
-            dispatch(actions.resetWorldToUniverse());
-            dispatch({ type: "increment graph render counter" });
+            dispatch(actions.resetSubsetAction());
           }}
         />
         {disableDiffexp ? null : <DiffexpButtons />}