mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-23 04:48:11 +08:00
* mocks for redux refactor - for discussion * more API design on redux refactor * add new reuqired dependencies for build * change babel target to use modern browser * remove dead code * remove dead code - joy plots * checkpoint on redux refactoring * checkpoint on redux refactoring * fix mistaken rebase conflict resolution * dead code removal; add name to dataframe backmap * rename dataframe to universe * update eslint config to more closely match prettier * lint * more eslint updates to match prettier * additional config to make eslint match prettier * add expression data to Universe/World * remove obsolete reducers * lint fixes * more eslint cleanup * lint * lint * fix but in countAllOnes when dimensions gt 1 * lint; do not display name metadata field * lint; colors refactor * lint; colors refactor * update comments * first cut at regraph and reset * enable object-curly-braces consistent mode * lint, handle regraph with no selection * fix expression scatterplot bugs * fix regression legend display * add expression data cache * remove console logging * reset cell color on regraph/reset * remove obsolete server URLs * rename UniverseV01 to Universe_REST_API_v01 * add additional comments on the varDataCache * merge universe reducer into controls reducer; simplify initialization-related actions * use spread operator * fix erroneous comment * convert universe and world state to plain objects, and functionalize supporting code (remove ES6 classes) * use spread operator * lint * improve variable names * rename obsCrossfilter to crossfilter and obsDimensionMap to dimensionMap * rename controls2 to controls
This commit is contained in:
Bruce Martin
+252
-182
@@ -1,101 +1,149 @@
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// jshint esversion: 6
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import _ from "lodash";
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import memoize from "memoize-one";
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import * as globals from "../globals";
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import store from "../reducers";
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import URI from "urijs";
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import _ from "lodash";
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import { Universe } from "../util/stateManager";
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const requestCells = (query = "") => {
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return dispatch => {
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dispatch({ type: "request cells started" });
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return fetch(`${globals.API.prefix}${globals.API.version}cells${query}`, {
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/*
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Catch unexpected errors and make sure we don't lose them!
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*/
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function catchErrorsWrap(fn) {
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return (dispatch, getState) => {
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fn(dispatch, getState).catch(error => {
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console.error(error);
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dispatch({ type: "UNEXPECTED ERROR", error });
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});
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};
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}
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async function doRequestInitialize() {
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const res = await fetch(
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`${globals.API.prefix}${globals.API.version}initialize`,
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{
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method: "get",
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headers: new Headers({
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"Content-Type": "application/json"
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})
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})
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.then(res => res.json())
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.then(
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data => dispatch({ type: "request cells success", data }),
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error => dispatch({ type: "request cells error", error })
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}
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);
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return res.json();
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}
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async function doRequestCells(query) {
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const res = await fetch(
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`${globals.API.prefix}${globals.API.version}cells${query}`,
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{
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method: "get",
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headers: new Headers({
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"Content-Type": "application/json"
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})
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}
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);
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return res.json();
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}
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function doInitialDataLoad(query = "") {
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return catchErrorsWrap(async dispatch => {
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dispatch({ type: "initial data load start" });
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try {
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const res = await Promise.all([
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doRequestInitialize(),
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doRequestCells(query)
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]);
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const universe = Universe.createUniverseFromRESTv01Response(
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res[0],
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res[1]
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);
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};
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};
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/* SELECT */
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const regraph = () => {
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return (dispatch, getState) => {
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dispatch({ type: "regraph started" });
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const state = getState();
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const selectedMetadata = {};
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_.each(state.controls.categoricalAsBooleansMap, (options, field) => {
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let atLeastOneOptionDeselected = false;
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_.each(options, (isActive, option) => {
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if (!isActive) {
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atLeastOneOptionDeselected = true;
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}
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dispatch({
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type: "initial data load complete (universe exists)",
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universe
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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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}
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});
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}
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if (atLeastOneOptionDeselected) {
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_.each(options, (isActive, option) => {
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if (isActive) {
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if (selectedMetadata[field]) {
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selectedMetadata[field].push(option);
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} else if (!selectedMetadata[field]) {
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selectedMetadata[field] = [option];
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}
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}
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});
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}
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});
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// XXX TODO - this is the old code for doing a regraph. Preserving it solely
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// until we port to 0.2 API. The new UX for regraph can't be implemented on
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// the 0.1 API (doesn't allow for re-layout on arbitrary sets of cells), so just
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// punting for now. See ticket #88
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//
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//
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// /* SELECT */
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// const regraph = () => {
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// return (dispatch, getState) => {
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// dispatch({ type: "regraph started" });
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//
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// const state = getState();
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// const selectedMetadata = {};
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//
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// _.each(state.controls.categoricalAsBooleansMap, (options, field) => {
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// let atLeastOneOptionDeselected = false;
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//
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// _.each(options, (isActive, option) => {
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// if (!isActive) {
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// atLeastOneOptionDeselected = true;
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// }
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// });
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//
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// if (atLeastOneOptionDeselected) {
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// _.each(options, (isActive, option) => {
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// if (isActive) {
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// if (selectedMetadata[field]) {
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// selectedMetadata[field].push(option);
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// } else if (!selectedMetadata[field]) {
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// selectedMetadata[field] = [option];
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// }
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// }
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// });
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// }
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// });
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//
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// let uri = new URI();
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// uri.setSearch(selectedMetadata);
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// console.log(uri.search(), selectedMetadata);
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//
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// dispatch(requestCells(uri.search())).then(res => {
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// if (res.error) {
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// dispatch({ type: "regraph error" });
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// } else {
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// dispatch({ type: "regraph success" });
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// }
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// });
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// };
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// };
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let uri = new URI();
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uri.setSearch(selectedMetadata);
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console.log(uri.search(), selectedMetadata);
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dispatch(requestCells(uri.search())).then(res => {
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if (res.error) {
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dispatch({ type: "regraph error" });
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} else {
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dispatch({ type: "regraph success" });
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}
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});
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};
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const regraph = () => (dispatch, getState) => {
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const { universe, world, crossfilter } = getState().controls;
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dispatch({
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type: "set World to current selection",
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universe,
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world,
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crossfilter
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});
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};
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const resetGraph = () => {
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return (dispatch, getState) => {
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dispatch({ type: "reset graph" });
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};
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};
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const initialize = () => {
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return (dispatch, getState) => {
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dispatch({ type: "initialize started" });
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fetch(`${globals.API.prefix}${globals.API.version}initialize`, {
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method: "get",
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headers: new Headers({
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"Content-Type": "application/json"
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})
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})
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.then(res => res.json())
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.then(
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data => dispatch({ type: "initialize success", data }),
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error => dispatch({ type: "initialize error", error })
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);
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};
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};
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const resetGraph = () => (dispatch, getState) =>
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dispatch({
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type: "reset World to eq Universe",
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universe: getState().controls.universe
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});
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// This code defends against the case where /expression returns a cellname
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// never seen before (ie, not returned by /cells). This should not happen
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// (see https://github.com/chanzuckerberg/cellxgene-rest-api/issues/34) but
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// occasionally does.
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//
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// XXX TODO - this code is only relevant in v0.1 REST API, and can be retired
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// when we port to 0.2.
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//
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const makeMetadataMap = memoize(metadata => _.keyBy(metadata, "CellName"));
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function cleanupExpressionResponse(data) {
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const s = store.getState();
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const metadata = s.controls.allCellsMetadataMap;
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const { universe } = s.controls;
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const metadata = makeMetadataMap(universe.obsAnnotations);
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let errorFound = false;
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data.data.cells = _.filter(data.data.cells, cell => {
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if (!errorFound && !metadata[cell.cellname]) {
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@@ -110,123 +158,145 @@ function cleanupExpressionResponse(data) {
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return data;
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}
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const requestGeneExpressionCounts = () => {
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return (dispatch, getState) => {
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dispatch({ type: "get expression started" });
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fetch(`${globals.API.prefix}${globals.API.version}expression`, {
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method: "get",
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headers: new Headers({
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accept: "application/json"
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})
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})
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.then(res => res.json())
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.then(data => cleanupExpressionResponse(data))
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.then(
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data => dispatch({ type: "get expression success", data }),
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error => dispatch({ type: "get expression error", error })
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);
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};
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};
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/*
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Fetch [gene, ...] from V0.1 API. Not an action function - just a helper
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which implements the new expression data caching.
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*/
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async function _doRequestExpressionData(dispatch, getState, genes) {
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const state = getState();
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/* check cache and only fetch data we do not already have */
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const { universe } = state.controls;
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const genesToFetch = _.filter(genes, g => !universe.varDataCache[g]);
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const requestSingleGeneExpressionCountsForColoringPOST = gene => {
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return (dispatch, getState) => {
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dispatch({ type: "get single gene expression for coloring started" });
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fetch(`${globals.API.prefix}${globals.API.version}expression`, {
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method: "POST",
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body: JSON.stringify({
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genelist: [gene]
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}),
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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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})
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.then(res => res.json())
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.then(data => cleanupExpressionResponse(data))
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.then(
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data =>
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dispatch({
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type: "color by expression",
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gene: gene,
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data
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dispatch({ type: "expression load start" });
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let expressionData = {}; // { gene: data }
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if (genesToFetch.length) {
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try {
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const res = await fetch(
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`${globals.API.prefix}${globals.API.version}expression`,
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{
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method: "POST",
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body: JSON.stringify({
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genelist: genes
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}),
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error =>
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dispatch({
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type: "get single gene expression for coloring error",
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error
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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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}
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);
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};
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};
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let data = await res.json();
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data = cleanupExpressionResponse(data);
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data = Universe.convertExpressionRESTv01ToObject(universe, data);
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expressionData = {
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...expressionData,
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...data
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};
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} catch (error) {
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dispatch({ type: "expression load error", error });
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throw error; // rethrow
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}
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}
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const requestGeneExpressionCountsPOST = genes => {
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return (dispatch, getState) => {
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dispatch({ type: "get expression started" });
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fetch(`${globals.API.prefix}${globals.API.version}expression`, {
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method: "POST",
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body: JSON.stringify({
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genelist: genes
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}),
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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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})
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.then(res => res.json())
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.then(data => cleanupExpressionResponse(data))
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.then(
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data => dispatch({ type: "get expression success", data }),
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error => dispatch({ type: "get expression error", error })
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);
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};
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};
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// add the cached values
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_.forEach(genes, g => {
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if (expressionData[g] === undefined) {
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expressionData[g] = universe.varDataCache[g];
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}
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});
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const requestDifferentialExpression = (celllist1, celllist2, num_genes = 7) => {
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return (dispatch, getState) => {
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dispatch({ type: "request differential expression started" });
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fetch(`${globals.API.prefix}${globals.API.version}diffexpression`, {
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method: "POST",
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body: JSON.stringify({
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celllist1,
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celllist2,
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num_genes
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}),
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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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})
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.then(res => res.json())
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.then(
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data => {
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/* kick off a secondary action to get all expression counts for all cells now that we know what the top expressed are */
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dispatch(
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requestGeneExpressionCountsPOST(
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_.union(
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data.data.celllist1.topgenes,
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data.data.celllist2.topgenes
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) // ["GPM6B", "FEZ1", "TSPAN31", "PCSK1N", "TUBA1A", "GPM6A", "CLU", "FCER1G", "TYROBP", "C1QB", "CD74", "CYBA", "GPX1", "TMSB4X"]
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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
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});
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return dispatch({ type: "expression load success", expressionData });
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}
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function requestSingleGeneExpressionCountsForColoringPOST(gene) {
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return async (dispatch, getState) => {
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dispatch({ type: "get single gene expression for coloring started" });
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try {
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await _doRequestExpressionData(dispatch, getState, [gene]);
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dispatch({
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type: "color by expression",
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gene,
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data: {
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[gene]: getState().controls.world.varDataCache[gene]
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}
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});
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} catch (error) {
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dispatch({
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type: "get single gene expression for coloring error",
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error
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});
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}
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};
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}
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const requestGeneExpressionCountsPOST = genes => async (dispatch, getState) => {
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dispatch({ type: "get expression started" });
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try {
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await _doRequestExpressionData(dispatch, getState, genes);
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return dispatch({
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type: "get expression success",
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genes,
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data: _.transform(
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genes,
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(res, gene) => {
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res[gene] = getState().controls.world.varDataCache[gene];
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},
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error =>
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dispatch({ type: "request differential expression error", error })
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);
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};
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{}
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)
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});
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} catch (error) {
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return dispatch({ type: "get expression error", error });
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}
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};
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const requestDifferentialExpression = (
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celllist1,
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celllist2,
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num_genes = 7
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) => dispatch => {
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dispatch({ type: "request differential expression started" });
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fetch(`${globals.API.prefix}${globals.API.version}diffexpression`, {
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method: "POST",
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body: JSON.stringify({
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celllist1,
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celllist2,
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num_genes
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}),
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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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||||
})
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.then(res => res.json())
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||||
.then(
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data => {
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/*
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kick off a secondary action to get all expression counts for all cells
|
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now that we know what the top expressed are
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*/
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dispatch(
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requestGeneExpressionCountsPOST(
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_.union(data.data.celllist1.topgenes, data.data.celllist2.topgenes)
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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
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||||
});
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||||
},
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||||
error =>
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||||
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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||||
export default {
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||||
initialize,
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||||
requestCells,
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||||
regraph,
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||||
resetGraph,
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||||
requestGeneExpressionCounts,
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||||
requestGeneExpressionCountsPOST,
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||||
requestSingleGeneExpressionCountsForColoringPOST,
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requestDifferentialExpression
|
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requestDifferentialExpression,
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doInitialDataLoad
|
||||
};
|
||||
|
||||
Reference in New Issue
Block a user