type catchErrorsWrap callsite

client/src/actions/embedding.ts

@@ -2,7 +2,9 @@
 action creators related to embeddings choice
 */
 
+import { Dispatch } from "redux";
 import { AnnoMatrixObsCrossfilter } from "../annoMatrix";
+import type { RootState } from "../reducers";
 import { _setEmbeddingSubset } from "../util/stateManager/viewStackHelpers";
 
 // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
@@ -29,30 +31,24 @@ export async function _switchEmbedding(
   return [annoMatrix, obsCrossfilter];
 }
 
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+export const layoutChoiceAction =
-export const layoutChoiceAction = (newLayoutChoice: any) => async (
+  (newLayoutChoice: string) =>
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+  async (dispatch: Dispatch, getState: () => RootState): Promise<void> => {
-  dispatch: any,
+    /*
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  getState: any
-) => {
-  /*
   On layout choice, make sure we have selected all on the previous layout, AND the new
   layout.
   */
-  const {
+    const { annoMatrix: prevAnnoMatrix, obsCrossfilter: prevCrossfilter } =
-    annoMatrix: prevAnnoMatrix,
+      getState();
-    obsCrossfilter: prevCrossfilter,
+    const [annoMatrix, obsCrossfilter] = await _switchEmbedding(
-  } = getState();
+      prevAnnoMatrix,
-  const [annoMatrix, obsCrossfilter] = await _switchEmbedding(
+      prevCrossfilter,
-    prevAnnoMatrix,
+      newLayoutChoice
-    prevCrossfilter,
+    );
-    newLayoutChoice
+    dispatch({
-  );
+      type: "set layout choice",
-  dispatch({
+      layoutChoice: newLayoutChoice,
-    type: "set layout choice",
+      obsCrossfilter,
-    layoutChoice: newLayoutChoice,
+      annoMatrix,
-    obsCrossfilter,
+    });
-    annoMatrix,
+  };
-  });
-};

client/src/actions/index.ts

@@ -1,3 +1,5 @@
+import { Dispatch } from "redux";
+
 import * as globals from "../globals";
 import { AnnoMatrixLoader, AnnoMatrixObsCrossfilter } from "../annoMatrix";
 import {
@@ -11,6 +13,8 @@ import * as annoActions from "./annotation";
 import * as viewActions from "./viewStack";
 import * as embActions from "./embedding";
 import * as genesetActions from "./geneset";
+import { LayoutColumn, Schema } from "../common/types/entities";
+import { RootState } from "../reducers";
 
 // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
 function setGlobalConfig(config: any) {
@@ -36,8 +40,8 @@ async function userColorsFetchAndLoad(dispatch: any) {
   );
 }
 
-async function schemaFetch() {
+async function schemaFetch(): Promise<{ schema: Schema }> {
-  return fetchJson("schema");
+  return (await fetchJson("schema")) as { schema: Schema };
 }
 
 // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
@@ -104,17 +108,17 @@ function prefetchEmbeddings(annoMatrix: any) {
 /*
 Application bootstrap
 */
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
+const doInitialDataLoad = (): ((
-const doInitialDataLoad = () =>
+  dispatch: Dispatch,
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+  getState: () => RootState
-  catchErrorsWrap(async (dispatch: any) => {
+) => void) =>
+  catchErrorsWrap(async (dispatch: Dispatch) => {
     dispatch({ type: "initial data load start" });
 
     try {
       const [config, schema] = await Promise.all([
         configFetch(dispatch),
-        // @ts-expect-error ts-migrate(2554) FIXME: Expected 0 arguments, but got 1.
+        schemaFetch(),
-        schemaFetch(dispatch),
         userColorsFetchAndLoad(dispatch),
         userInfoFetch(dispatch),
       ]);
@@ -137,10 +141,9 @@ const doInitialDataLoad = () =>
       const layoutSchema = schema?.schema?.layout?.obs ?? [];
       if (
         defaultEmbedding &&
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+        layoutSchema.some((s: LayoutColumn) => s.name === defaultEmbedding)
-        layoutSchema.some((s: any) => s.name === defaultEmbedding)
       ) {
-        dispatch(embActions.layoutChoiceAction(defaultEmbedding));
+        embActions.layoutChoiceAction(defaultEmbedding);
       }
     } catch (error) {
       dispatch({ type: "initial data load error", error });
@@ -188,84 +191,85 @@ const dispatchDiffExpErrors = (dispatch: any, response: any) => {
   }
 };
 
-const requestDifferentialExpression = (
+const requestDifferentialExpression =
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+  (
-  set1: any,
+    // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+    set1: any,
-  set2: any,
+    // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  num_genes = 50
+    set2: any,
-  // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+    num_genes = 50
-) => async (dispatch: any, getState: any) => {
+    // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
-  dispatch({ type: "request differential expression started" });
+  ) =>
-  try {
+  async (dispatch: any, getState: any) => {
-    /*
+    dispatch({ type: "request differential expression started" });
+    try {
+      /*
     Steps:
     1. get the most differentially expressed genes
     2. get expression data for each
     */
-    const { annoMatrix } = getState();
+      const { annoMatrix } = getState();
-    const varIndexName = annoMatrix.schema.annotations.var.index;
+      const varIndexName = annoMatrix.schema.annotations.var.index;
 
-    // Legal values are null, Array or TypedArray.  Null is initial state.
+      // Legal values are null, Array or TypedArray.  Null is initial state.
-    if (!set1) set1 = [];
+      if (!set1) set1 = [];
-    if (!set2) set2 = [];
+      if (!set2) set2 = [];
 
-    // These lines ensure that we convert any TypedArray to an Array.
+      // These lines ensure that we convert any TypedArray to an Array.
-    // This is necessary because JSON.stringify() does some very strange
+      // This is necessary because JSON.stringify() does some very strange
-    // things with TypedArrays (they are marshalled to JSON objects, rather
+      // things with TypedArrays (they are marshalled to JSON objects, rather
-    // than being marshalled as a JSON array).
+      // than being marshalled as a JSON array).
-    set1 = Array.isArray(set1) ? set1 : Array.from(set1);
+      set1 = Array.isArray(set1) ? set1 : Array.from(set1);
-    set2 = Array.isArray(set2) ? set2 : Array.from(set2);
+      set2 = Array.isArray(set2) ? set2 : Array.from(set2);
 
-    const res = await fetch(
+      const res = await fetch(
-      `${globals.API.prefix}${globals.API.version}diffexp/obs`,
+        `${globals.API.prefix}${globals.API.version}diffexp/obs`,
-      {
+        {
-        method: "POST",
+          method: "POST",
-        headers: new Headers({
+          headers: new Headers({
-          Accept: "application/json",
+            Accept: "application/json",
-          "Content-Type": "application/json",
+            "Content-Type": "application/json",
-        }),
+          }),
-        body: JSON.stringify({
+          body: JSON.stringify({
-          mode: "topN",
+            mode: "topN",
-          count: num_genes,
+            count: num_genes,
-          set1: { filter: { obs: { index: set1 } } },
+            set1: { filter: { obs: { index: set1 } } },
-          set2: { filter: { obs: { index: set2 } } },
+            set2: { filter: { obs: { index: set2 } } },
-        }),
+          }),
-        credentials: "include",
+          credentials: "include",
+        }
+      );
+
+      if (!res.ok || res.headers.get("Content-Type") !== "application/json") {
+        return dispatchDiffExpErrors(dispatch, res);
       }
-    );
 
-    if (!res.ok || res.headers.get("Content-Type") !== "application/json") {
+      const response = await res.json();
-      return dispatchDiffExpErrors(dispatch, res);
+      const varIndex = await annoMatrix.fetch("var", varIndexName);
+      const diffexpLists = { negative: [], positive: [] };
+      for (const polarity of Object.keys(diffexpLists)) {
+        // @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message
+        // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
+        diffexpLists[polarity] = response[polarity].map((v: any) => [
+          varIndex.at(v[0], varIndexName),
+          ...v.slice(1),
+        ]);
+      }
+
+      /* then send the success case action through */
+      return dispatch({
+        type: "request differential expression success",
+        data: diffexpLists,
+      });
+    } catch (error) {
+      return dispatch({
+        type: "request differential expression error",
+        error,
+      });
     }
+  };
 
-    const response = await res.json();
+function fetchJson(pathAndQuery: string) {
-    const varIndex = await annoMatrix.fetch("var", varIndexName);
-    const diffexpLists = { negative: [], positive: [] };
-    for (const polarity of Object.keys(diffexpLists)) {
-      // @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-      diffexpLists[polarity] = response[polarity].map((v: any) => [
-        varIndex.at(v[0], varIndexName),
-        ...v.slice(1),
-      ]);
-    }
-
-    /* then send the success case action through */
-    return dispatch({
-      type: "request differential expression success",
-      data: diffexpLists,
-    });
-  } catch (error) {
-    return dispatch({
-      type: "request differential expression error",
-      error,
-    });
-  }
-};
-
-// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
-function fetchJson(pathAndQuery: any) {
   return doJsonRequest(
     `${globals.API.prefix}${globals.API.version}${pathAndQuery}`
   );

client/src/components/framework/toasters.ts

@@ -26,8 +26,10 @@ export const keepAroundErrorToast = (message: any) =>
 /*
 a hard network error
 */
-// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
+export const postNetworkErrorToast = (
-export const postNetworkErrorToast = (message: any, key = undefined) =>
+  message: string,
+  key: string | undefined = undefined
+): string =>
   ToastTopCenter.show(
     {
       message,