re-implement re-embeddings (#1679)

* fix mispelling

* re-implement re-embedding

* always load base embedding to fetch counts

* format

* lint

* fix tests

* lint

* fix accept handling

* test log

* more debug

* more

* more

* more

* more

* remove logging

* logging

* jsonify

* remove debugging logs

* lint

* clean up errors a bit

* fix issue found in PR review

* PR review changes

client/src/actions/embedding.js

@@ -5,6 +5,23 @@ action creators related to embeddings choice
 import { AnnoMatrixObsCrossfilter } from "../annoMatrix";
 import { _setEmbeddingSubset } from "../util/stateManager/viewStackHelpers";
 
+export async function _switchEmbedding(prevAnnoMatrix, newEmbeddingName) {
+  /*
+  DRY helper used by this and reembedding action creators
+  */
+  const base = prevAnnoMatrix.base();
+  const embeddingDf = await base.fetch("emb", newEmbeddingName);
+  const annoMatrix = _setEmbeddingSubset(prevAnnoMatrix, embeddingDf);
+  const obsCrossfilter = await new AnnoMatrixObsCrossfilter(annoMatrix).select(
+    "emb",
+    newEmbeddingName,
+    {
+      mode: "all",
+    }
+  );
+  return [annoMatrix, obsCrossfilter];
+}
+
 export const layoutChoiceAction = (newLayoutChoice) => async (
   dispatch,
   getState
@@ -14,15 +31,9 @@ export const layoutChoiceAction = (newLayoutChoice) => async (
   layout.
   */
   const { annoMatrix: prevAnnoMatrix } = getState();
-
-  const embeddingDf = await prevAnnoMatrix.base().fetch("emb", newLayoutChoice);
-  const annoMatrix = _setEmbeddingSubset(prevAnnoMatrix, embeddingDf);
-  const obsCrossfilter = await new AnnoMatrixObsCrossfilter(annoMatrix).select(
-    "emb",
-    newLayoutChoice,
-    {
-      mode: "all",
-    }
+  const [annoMatrix, obsCrossfilter] = await _switchEmbedding(
+    prevAnnoMatrix,
+    newLayoutChoice
   );
   dispatch({
     type: "set layout choice",

client/src/actions/reembed.js

@@ -1,10 +1,10 @@
 import { API } from "../globals";
-import { MatrixFBS } from "../util/stateManager";
 import {
   postNetworkErrorToast,
   postAsyncSuccessToast,
   postAsyncFailureToast,
 } from "../components/framework/toasters";
+import { _switchEmbedding } from "./embedding";
 
 function abortableFetch(request, opts, timeout = 0) {
   const controller = new AbortController();
@@ -24,7 +24,7 @@ function abortableFetch(request, opts, timeout = 0) {
 
 async function doReembedFetch(dispatch, getState) {
   const state = getState();
-  let cells = state.world.obsAnnotations.rowIndex.labels();
+  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
@@ -54,10 +54,7 @@ async function doReembedFetch(dispatch, getState) {
   });
   const res = await af.ready();
 
-  if (
-    res.ok &&
-    res.headers.get("Content-Type").includes("application/octet-stream")
-  ) {
+  if (res.ok && res.headers.get("Content-Type").includes("application/json")) {
     return res;
   }
 
@@ -67,7 +64,6 @@ async function doReembedFetch(dispatch, getState) {
   if (body && body.length > 0) {
     msg = `${msg} -- ${body}`;
   }
-  postNetworkErrorToast(msg);
   throw new Error(msg);
 }
 
@@ -78,17 +74,24 @@ export function requestReembed() {
   return async (dispatch, getState) => {
     try {
       const res = await doReembedFetch(dispatch, getState);
-      const schema = JSON.parse(res.headers.get("CxG-Schema"));
-      const buffer = await res.arrayBuffer();
-      const df = MatrixFBS.matrixFBSToDataframe(buffer);
+      const schema = await res.json();
       dispatch({
         type: "reembed: request completed",
       });
+
+      const { annoMatrix: prevAnnoMatrix } = getState();
+      const base = prevAnnoMatrix.base().addEmbedding(schema);
+      const [annoMatrix, obsCrossfilter] = await _switchEmbedding(
+        base,
+        schema.name
+      );
       dispatch({
         type: "reembed: add reembedding",
-        embedding: df,
         schema,
+        annoMatrix,
+        obsCrossfilter,
       });
+
       postAsyncSuccessToast("Re-embedding has completed.");
     } catch (error) {
       dispatch({
@@ -103,13 +106,3 @@ export function requestReembed() {
     }
   };
 }
-
-/* disabled until reimplementation occurs
-export function reembedResetWorldToUniverse(dispatch, getState) {
-  const { reembedController } = getState();
-  if (reembedController.pendingFetch) reembedController.pendingFetch.abort();
-  dispatch({
-    type: "reembed: clear all reembeddings",
-  });
-}
-*/