remove experimental reembedding support (#2301)

* remove experimental reembedding support

* lint

* lint

* add prepare requirements to requirements-dev

* oops, revert accidental deletion of import

* more test modifications

* remove obsolete unit tests

client/src/actions/embedding.js

@@ -11,7 +11,7 @@ export async function _switchEmbedding(
   newEmbeddingName
 ) {
   /*
-  DRY helper used by this and reembedding action creators
+  DRY helper used by embedding action creators
   */
   const base = prevAnnoMatrix.base();
   const embeddingDf = await base.fetch("emb", newEmbeddingName);

client/src/actions/index.js

@@ -5,9 +5,6 @@ import {
   doJsonRequest,
   dispatchNetworkErrorMessageToUser,
 } from "../util/actionHelpers";
-import {
-  requestReembed /* , reembedResetWorldToUniverse -- disabled temporarily, TODO issue #1606 */,
-} from "./reembed";
 import { loadUserColorConfig } from "../util/stateManager/colorHelpers";
 import * as selnActions from "./selection";
 import * as annoActions from "./annotation";
@@ -243,7 +240,6 @@ export default {
   requestDifferentialExpression,
   requestSingleGeneExpressionCountsForColoringPOST,
   requestUserDefinedGene,
-  requestReembed,
   selectContinuousMetadataAction: selnActions.selectContinuousMetadataAction,
   selectCategoricalMetadataAction: selnActions.selectCategoricalMetadataAction,
   selectCategoricalAllMetadataAction:

client/src/actions/reembed.js

@@ -1,112 +0,0 @@
-import { API } from "../globals";
-import {
-  postNetworkErrorToast,
-  postAsyncSuccessToast,
-  postAsyncFailureToast,
-} from "../components/framework/toasters";
-import { _switchEmbedding } from "./embedding";
-
-function abortableFetch(request, opts, timeout = 0) {
-  const controller = new AbortController();
-  const { signal } = controller;
-
-  return {
-    abort: () => controller.abort(),
-    isAborted: () => signal.aborted,
-    ready: () => {
-      if (timeout) {
-        setTimeout(() => controller.abort(), timeout);
-      }
-      return fetch(request, { ...opts, signal });
-    },
-  };
-}
-
-async function doReembedFetch(dispatch, getState) {
-  const state = getState();
-  let cells = state.annoMatrix.rowIndex.labels();
-
-  // These lines ensure that we convert any TypedArray to an Array.
-  // This is necessary because JSON.stringify() does some very strange
-  // things with TypedArrays (they are marshalled to JSON objects, rather
-  // than being marshalled as a JSON array).
-  cells = Array.isArray(cells) ? cells : Array.from(cells);
-
-  const af = abortableFetch(
-    `${API.prefix}${API.version}layout/obs`,
-    {
-      method: "PUT",
-      headers: new Headers({
-        Accept: "application/octet-stream",
-        "Content-Type": "application/json",
-      }),
-      body: JSON.stringify({
-        method: "umap",
-        filter: { obs: { index: cells } },
-      }),
-      credentials: "include",
-    },
-    60000 // 1 minute timeout
-  );
-  dispatch({
-    type: "reembed: request start",
-    abortableFetch: af,
-  });
-  const res = await af.ready();
-
-  if (res.ok && res.headers.get("Content-Type").includes("application/json")) {
-    return res;
-  }
-
-  // else an error
-  let msg = `Unexpected HTTP response ${res.status}, ${res.statusText}`;
-  const body = await res.text();
-  if (body && body.length > 0) {
-    msg = `${msg} -- ${body}`;
-  }
-  throw new Error(msg);
-}
-
-/*
-functions below are dispatch-able
-*/
-export function requestReembed() {
-  return async (dispatch, getState) => {
-    try {
-      const res = await doReembedFetch(dispatch, getState);
-      const schema = await res.json();
-      dispatch({
-        type: "reembed: request completed",
-      });
-
-      const {
-        annoMatrix: prevAnnoMatrix,
-        obsCrossfilter: prevCrossfilter,
-      } = getState();
-      const base = prevAnnoMatrix.base().addEmbedding(schema);
-      const [annoMatrix, obsCrossfilter] = await _switchEmbedding(
-        base,
-        prevCrossfilter,
-        schema.name
-      );
-      dispatch({
-        type: "reembed: add reembedding",
-        schema,
-        annoMatrix,
-        obsCrossfilter,
-      });
-
-      postAsyncSuccessToast("Re-embedding has completed.");
-    } catch (error) {
-      dispatch({
-        type: "reembed: request aborted",
-      });
-      if (error.name === "AbortError") {
-        postAsyncFailureToast("Re-embedding calculation was aborted.");
-      } else {
-        postNetworkErrorToast(`Re-embedding: ${error.message}`);
-      }
-      console.log("Reembed exception:", error, error.name, error.message);
-    }
-  };
-}

client/src/components/menubar/index.js

@@ -11,7 +11,6 @@ import AuthButtons from "./authButtons";
 import Subset from "./subset";
 import UndoRedoReset from "./undoRedo";
 import DiffexpButtons from "./diffexpButtons";
-import Reembedding from "./reembedding";
 import { getEmbSubsetView } from "../../util/stateManager/viewStackHelpers";
 
 @connect((state) => {
@@ -49,8 +48,6 @@ import { getEmbSubsetView } from "../../util/stateManager/viewStackHelpers";
     tosURL: state.config?.parameters?.about_legal_tos,
     privacyURL: state.config?.parameters?.about_legal_privacy,
     categoricalSelection: state.categoricalSelection,
-    enableReembedding:
-      state.config?.parameters?.["enable-reembedding"] ?? false,
   };
 })
 class MenuBar extends React.PureComponent {
@@ -212,7 +209,6 @@ class MenuBar extends React.PureComponent {
       colorAccessor,
       subsetPossible,
       subsetResetPossible,
-      enableReembedding,
       userInfo,
       auth,
     } = this.props;
@@ -262,7 +258,6 @@ class MenuBar extends React.PureComponent {
             this.handleClipPercentileMinValueChange
           }
         />
-        {enableReembedding ? <Reembedding /> : null}
         <Tooltip
           content="When a category is colored by, show labels on the graph"
           position="bottom"

client/src/components/menubar/reembedding.js

@@ -1,40 +0,0 @@
-import React from "react";
-import { connect } from "react-redux";
-import { AnchorButton, ButtonGroup, Tooltip } from "@blueprintjs/core";
-import * as globals from "../../globals";
-import actions from "../../actions";
-import styles from "./menubar.css";
-
-@connect((state) => ({
-  reembedController: state.reembedController,
-  annoMatrix: state.annoMatrix,
-}))
-class Reembedding extends React.PureComponent {
-  render() {
-    const { dispatch, annoMatrix, reembedController } = this.props;
-    const loading = !!reembedController?.pendingFetch;
-    const disabled = annoMatrix.nObs === annoMatrix.schema.dataframe.nObs;
-    const tipContent = disabled
-      ? "Subset cells first, then click to recompute UMAP embedding."
-      : "Click to recompute UMAP embedding on the current cell subset.";
-
-    return (
-      <ButtonGroup className={styles.menubarButton}>
-        <Tooltip
-          content={tipContent}
-          position="bottom"
-          hoverOpenDelay={globals.tooltipHoverOpenDelay}
-        >
-          <AnchorButton
-            icon="new-object"
-            disabled={disabled}
-            onClick={() => dispatch(actions.requestReembed())}
-            loading={loading}
-          />
-        </Tooltip>
-      </ButtonGroup>
-    );
-  }
-}
-
-export default Reembedding;

client/src/reducers/index.js

@@ -20,7 +20,6 @@ import genesetsUI from "./genesetsUI";
 import autosave from "./autosave";
 import centroidLabels from "./centroidLabels";
 import pointDialation from "./pointDilation";
-import { reembedController } from "./reembed";
 import { gcMiddleware as annoMatrixGC } from "../annoMatrix";
 
 import undoableConfig from "./undoableConfig";
@@ -42,7 +41,6 @@ const Reducer = undoable(
     ["differential", differential],
     ["centroidLabels", centroidLabels],
     ["pointDilation", pointDialation],
-    ["reembedController", reembedController],
     ["autosave", autosave],
     ["userInfo", userInfo],
   ]),

client/src/reducers/layoutChoice.js

@@ -47,19 +47,6 @@ const LayoutChoice = (
       return { ...state, current, currentDimNames };
     }
 
-    case "reembed: add reembedding": {
-      const { schema } = nextSharedState.annoMatrix;
-      const { name } = action.schema;
-      const available = Array.from(new Set(state.available).add(name));
-      const currentDimNames = schema.layout.obsByName[name].dims;
-      return {
-        ...state,
-        available,
-        current: name,
-        currentDimNames,
-      };
-    }
-
     default: {
       return state;
     }

client/src/reducers/reembed.js

@@ -1,29 +0,0 @@
-/*
-controller state is not part of the undo/redo history
-*/
-export const reembedController = (
-  state = {
-    pendingFetch: null,
-  },
-  action
-) => {
-  switch (action.type) {
-    case "reembed: request start": {
-      return {
-        ...state,
-        pendingFetch: action.abortableFetch,
-      };
-    }
-    case "reembed: request aborted":
-    case "reembed: request cancel":
-    case "reembed: request completed": {
-      return {
-        ...state,
-        pendingFetch: null,
-      };
-    }
-    default: {
-      return state;
-    }
-  }
-};