mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-24 23:28:12 +08:00
type catchErrorsWrap callsite
This commit is contained in:
Seve Badajoz
@@ -2,7 +2,9 @@
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action creators related to embeddings choice
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*/
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import { Dispatch } from "redux";
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import { AnnoMatrixObsCrossfilter } from "../annoMatrix";
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import type { RootState } from "../reducers";
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import { _setEmbeddingSubset } from "../util/stateManager/viewStackHelpers";
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// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
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@@ -29,30 +31,24 @@ export async function _switchEmbedding(
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return [annoMatrix, obsCrossfilter];
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}
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// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
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export const layoutChoiceAction = (newLayoutChoice: any) => async (
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// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
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dispatch: any,
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// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
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getState: any
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) => {
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/*
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export const layoutChoiceAction =
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(newLayoutChoice: string) =>
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async (dispatch: Dispatch, getState: () => RootState): Promise<void> => {
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/*
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On layout choice, make sure we have selected all on the previous layout, AND the new
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layout.
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*/
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const {
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annoMatrix: prevAnnoMatrix,
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obsCrossfilter: prevCrossfilter,
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} = getState();
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const [annoMatrix, obsCrossfilter] = await _switchEmbedding(
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prevAnnoMatrix,
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prevCrossfilter,
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newLayoutChoice
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);
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dispatch({
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type: "set layout choice",
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layoutChoice: newLayoutChoice,
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obsCrossfilter,
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annoMatrix,
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});
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};
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const { annoMatrix: prevAnnoMatrix, obsCrossfilter: prevCrossfilter } =
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getState();
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const [annoMatrix, obsCrossfilter] = await _switchEmbedding(
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prevAnnoMatrix,
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prevCrossfilter,
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newLayoutChoice
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);
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dispatch({
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type: "set layout choice",
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layoutChoice: newLayoutChoice,
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obsCrossfilter,
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annoMatrix,
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});
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};
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+82
-78
@@ -1,3 +1,5 @@
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import { Dispatch } from "redux";
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import * as globals from "../globals";
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import { AnnoMatrixLoader, AnnoMatrixObsCrossfilter } from "../annoMatrix";
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import {
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@@ -11,6 +13,8 @@ import * as annoActions from "./annotation";
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import * as viewActions from "./viewStack";
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import * as embActions from "./embedding";
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import * as genesetActions from "./geneset";
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import { LayoutColumn, Schema } from "../common/types/entities";
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import { RootState } from "../reducers";
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// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
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function setGlobalConfig(config: any) {
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@@ -36,8 +40,8 @@ async function userColorsFetchAndLoad(dispatch: any) {
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);
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}
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async function schemaFetch() {
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return fetchJson("schema");
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async function schemaFetch(): Promise<{ schema: Schema }> {
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return (await fetchJson("schema")) as { schema: Schema };
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}
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// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
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@@ -104,17 +108,17 @@ function prefetchEmbeddings(annoMatrix: any) {
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/*
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Application bootstrap
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*/
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// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
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const doInitialDataLoad = () =>
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// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
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catchErrorsWrap(async (dispatch: any) => {
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const doInitialDataLoad = (): ((
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dispatch: Dispatch,
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getState: () => RootState
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) => void) =>
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catchErrorsWrap(async (dispatch: Dispatch) => {
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dispatch({ type: "initial data load start" });
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try {
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const [config, schema] = await Promise.all([
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configFetch(dispatch),
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// @ts-expect-error ts-migrate(2554) FIXME: Expected 0 arguments, but got 1.
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schemaFetch(dispatch),
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schemaFetch(),
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userColorsFetchAndLoad(dispatch),
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userInfoFetch(dispatch),
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]);
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@@ -137,10 +141,9 @@ const doInitialDataLoad = () =>
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const layoutSchema = schema?.schema?.layout?.obs ?? [];
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if (
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defaultEmbedding &&
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// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
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layoutSchema.some((s: any) => s.name === defaultEmbedding)
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layoutSchema.some((s: LayoutColumn) => s.name === defaultEmbedding)
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) {
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dispatch(embActions.layoutChoiceAction(defaultEmbedding));
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embActions.layoutChoiceAction(defaultEmbedding);
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}
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} catch (error) {
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dispatch({ type: "initial data load error", error });
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@@ -188,84 +191,85 @@ const dispatchDiffExpErrors = (dispatch: any, response: any) => {
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}
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};
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const requestDifferentialExpression = (
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// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
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set1: any,
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// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
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set2: any,
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num_genes = 50
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// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
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) => async (dispatch: any, getState: any) => {
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dispatch({ type: "request differential expression started" });
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try {
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/*
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const requestDifferentialExpression =
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(
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// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
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set1: any,
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// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
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set2: any,
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num_genes = 50
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// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
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) =>
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async (dispatch: any, getState: any) => {
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dispatch({ type: "request differential expression started" });
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try {
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/*
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Steps:
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1. get the most differentially expressed genes
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2. get expression data for each
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*/
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const { annoMatrix } = getState();
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const varIndexName = annoMatrix.schema.annotations.var.index;
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const { annoMatrix } = getState();
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const varIndexName = annoMatrix.schema.annotations.var.index;
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// Legal values are null, Array or TypedArray. Null is initial state.
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if (!set1) set1 = [];
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if (!set2) set2 = [];
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// Legal values are null, Array or TypedArray. Null is initial state.
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if (!set1) set1 = [];
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if (!set2) set2 = [];
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// These lines ensure that we convert any TypedArray to an Array.
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// This is necessary because JSON.stringify() does some very strange
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// things with TypedArrays (they are marshalled to JSON objects, rather
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// than being marshalled as a JSON array).
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set1 = Array.isArray(set1) ? set1 : Array.from(set1);
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set2 = Array.isArray(set2) ? set2 : Array.from(set2);
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// These lines ensure that we convert any TypedArray to an Array.
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// This is necessary because JSON.stringify() does some very strange
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// things with TypedArrays (they are marshalled to JSON objects, rather
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// than being marshalled as a JSON array).
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set1 = Array.isArray(set1) ? set1 : Array.from(set1);
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set2 = Array.isArray(set2) ? set2 : Array.from(set2);
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const res = await fetch(
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`${globals.API.prefix}${globals.API.version}diffexp/obs`,
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{
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method: "POST",
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headers: new Headers({
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Accept: "application/json",
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"Content-Type": "application/json",
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}),
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body: JSON.stringify({
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mode: "topN",
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count: num_genes,
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set1: { filter: { obs: { index: set1 } } },
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set2: { filter: { obs: { index: set2 } } },
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}),
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credentials: "include",
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const res = await fetch(
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`${globals.API.prefix}${globals.API.version}diffexp/obs`,
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{
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method: "POST",
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headers: new Headers({
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Accept: "application/json",
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"Content-Type": "application/json",
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}),
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body: JSON.stringify({
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mode: "topN",
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count: num_genes,
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set1: { filter: { obs: { index: set1 } } },
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set2: { filter: { obs: { index: set2 } } },
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}),
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credentials: "include",
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}
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);
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if (!res.ok || res.headers.get("Content-Type") !== "application/json") {
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return dispatchDiffExpErrors(dispatch, res);
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}
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);
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if (!res.ok || res.headers.get("Content-Type") !== "application/json") {
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return dispatchDiffExpErrors(dispatch, res);
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const response = await res.json();
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const varIndex = await annoMatrix.fetch("var", varIndexName);
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const diffexpLists = { negative: [], positive: [] };
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for (const polarity of Object.keys(diffexpLists)) {
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// @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message
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// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
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diffexpLists[polarity] = response[polarity].map((v: any) => [
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varIndex.at(v[0], varIndexName),
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...v.slice(1),
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]);
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}
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/* then send the success case action through */
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return dispatch({
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type: "request differential expression success",
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data: diffexpLists,
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});
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} catch (error) {
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return dispatch({
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type: "request differential expression error",
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error,
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});
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}
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};
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const response = await res.json();
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const varIndex = await annoMatrix.fetch("var", varIndexName);
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const diffexpLists = { negative: [], positive: [] };
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for (const polarity of Object.keys(diffexpLists)) {
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// @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message
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// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
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diffexpLists[polarity] = response[polarity].map((v: any) => [
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varIndex.at(v[0], varIndexName),
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...v.slice(1),
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]);
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}
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/* then send the success case action through */
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return dispatch({
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type: "request differential expression success",
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data: diffexpLists,
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});
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} catch (error) {
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return dispatch({
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type: "request differential expression error",
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error,
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});
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}
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};
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// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
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function fetchJson(pathAndQuery: any) {
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function fetchJson(pathAndQuery: string) {
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return doJsonRequest(
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`${globals.API.prefix}${globals.API.version}${pathAndQuery}`
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);
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@@ -26,8 +26,10 @@ export const keepAroundErrorToast = (message: any) =>
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/*
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a hard network error
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*/
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// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
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export const postNetworkErrorToast = (message: any, key = undefined) =>
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export const postNetworkErrorToast = (
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message: string,
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key: string | undefined = undefined
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): string =>
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ToastTopCenter.show(
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{
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message,
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