mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-10-06 06:58:12 +08:00
* Added TS. Updated build and linting config. Added types. * [ts-migrate][.] Rename files from JS/JSX to TS/TSX Co-authored-by: ts-migrate <> * [ts-migrate][.] Run TS Migrate Co-authored-by: ts-migrate <> * Corrected files mangled by ts-migrate. * Updated lint config, minor linting. * Re-enabled Husky. * Updated tests and config. * Reverted webpack devtool config. * Removed obsolete snapshots. * Added annotations snap. * Updated tsconfig includes wrt linting. * Removed ts-migrate. Co-authored-by: Timmy Huang <tihuan@users.noreply.github.com>
This commit is contained in:
Mim Hastie
co-authored by
ts-migrate
Timmy Huang
ts-migrate
Timmy Huang
parent
7328cbdbd5
commit
934cc5c69b
@@ -1,275 +0,0 @@
|
||||
import * as globals from "../globals";
|
||||
import { AnnoMatrixLoader, AnnoMatrixObsCrossfilter } from "../annoMatrix";
|
||||
import {
|
||||
catchErrorsWrap,
|
||||
doJsonRequest,
|
||||
dispatchNetworkErrorMessageToUser,
|
||||
} from "../util/actionHelpers";
|
||||
import { loadUserColorConfig } from "../util/stateManager/colorHelpers";
|
||||
import * as selnActions from "./selection";
|
||||
import * as annoActions from "./annotation";
|
||||
import * as viewActions from "./viewStack";
|
||||
import * as embActions from "./embedding";
|
||||
import * as genesetActions from "./geneset";
|
||||
|
||||
/*
|
||||
return promise fetching user-configured colors
|
||||
*/
|
||||
async function userColorsFetchAndLoad(dispatch) {
|
||||
return fetchJson("colors").then((response) =>
|
||||
dispatch({
|
||||
type: "universe: user color load success",
|
||||
userColors: loadUserColorConfig(response),
|
||||
})
|
||||
);
|
||||
}
|
||||
|
||||
async function schemaFetch() {
|
||||
return fetchJson("schema");
|
||||
}
|
||||
|
||||
async function configFetch(dispatch) {
|
||||
return fetchJson("config").then((response) => {
|
||||
const config = { ...globals.configDefaults, ...response.config };
|
||||
dispatch({
|
||||
type: "configuration load complete",
|
||||
config,
|
||||
});
|
||||
return config;
|
||||
});
|
||||
}
|
||||
|
||||
async function userInfoFetch(dispatch) {
|
||||
return fetchJson("userinfo").then((response) => {
|
||||
const { userinfo: userInfo } = response || {};
|
||||
dispatch({
|
||||
type: "userInfo load complete",
|
||||
userInfo,
|
||||
});
|
||||
return userInfo;
|
||||
});
|
||||
}
|
||||
|
||||
async function genesetsFetch(dispatch, config) {
|
||||
/* request genesets ONLY if the backend supports the feature */
|
||||
const defaultResponse = {
|
||||
genesets: [],
|
||||
tid: 0,
|
||||
};
|
||||
if (config?.parameters?.annotations_genesets ?? false) {
|
||||
fetchJson("genesets").then((response) => {
|
||||
dispatch({
|
||||
type: "geneset: initial load",
|
||||
data: response ?? defaultResponse,
|
||||
});
|
||||
});
|
||||
} else {
|
||||
dispatch({
|
||||
type: "geneset: initial load",
|
||||
data: defaultResponse,
|
||||
});
|
||||
}
|
||||
}
|
||||
|
||||
function prefetchEmbeddings(annoMatrix) {
|
||||
/*
|
||||
prefetch requests for all embeddings
|
||||
*/
|
||||
const { schema } = annoMatrix;
|
||||
const available = schema.layout.obs.map((v) => v.name);
|
||||
available.forEach((embName) => annoMatrix.prefetch("emb", embName));
|
||||
}
|
||||
|
||||
/*
|
||||
Application bootstrap
|
||||
*/
|
||||
const doInitialDataLoad = () =>
|
||||
catchErrorsWrap(async (dispatch) => {
|
||||
dispatch({ type: "initial data load start" });
|
||||
|
||||
try {
|
||||
const [config, schema] = await Promise.all([
|
||||
configFetch(dispatch),
|
||||
schemaFetch(dispatch),
|
||||
userColorsFetchAndLoad(dispatch),
|
||||
userInfoFetch(dispatch),
|
||||
]);
|
||||
|
||||
genesetsFetch(dispatch, config);
|
||||
|
||||
const baseDataUrl = `${globals.API.prefix}${globals.API.version}`;
|
||||
const annoMatrix = new AnnoMatrixLoader(baseDataUrl, schema.schema);
|
||||
const obsCrossfilter = new AnnoMatrixObsCrossfilter(annoMatrix);
|
||||
prefetchEmbeddings(annoMatrix);
|
||||
|
||||
dispatch({
|
||||
type: "annoMatrix: init complete",
|
||||
annoMatrix,
|
||||
obsCrossfilter,
|
||||
});
|
||||
dispatch({ type: "initial data load complete" });
|
||||
|
||||
const defaultEmbedding = config?.parameters?.default_embedding;
|
||||
const layoutSchema = schema?.schema?.layout?.obs ?? [];
|
||||
if (
|
||||
defaultEmbedding &&
|
||||
layoutSchema.some((s) => s.name === defaultEmbedding)
|
||||
) {
|
||||
dispatch(embActions.layoutChoiceAction(defaultEmbedding));
|
||||
}
|
||||
} catch (error) {
|
||||
dispatch({ type: "initial data load error", error });
|
||||
}
|
||||
}, true);
|
||||
|
||||
function requestSingleGeneExpressionCountsForColoringPOST(gene) {
|
||||
return {
|
||||
type: "color by expression",
|
||||
gene,
|
||||
};
|
||||
}
|
||||
|
||||
const requestUserDefinedGene = (gene) => ({
|
||||
type: "request user defined gene success",
|
||||
data: {
|
||||
genes: [gene],
|
||||
},
|
||||
});
|
||||
|
||||
const dispatchDiffExpErrors = (dispatch, response) => {
|
||||
switch (response.status) {
|
||||
case 403:
|
||||
dispatchNetworkErrorMessageToUser(
|
||||
"Too many cells selected for differential experesion calculation - please make a smaller selection."
|
||||
);
|
||||
break;
|
||||
case 501:
|
||||
dispatchNetworkErrorMessageToUser(
|
||||
"Differential expression is not implemented."
|
||||
);
|
||||
break;
|
||||
default: {
|
||||
const msg = `Unexpected differential expression HTTP response ${response.status}, ${response.statusText}`;
|
||||
dispatchNetworkErrorMessageToUser(msg);
|
||||
dispatch({
|
||||
type: "request differential expression error",
|
||||
error: new Error(msg),
|
||||
});
|
||||
}
|
||||
}
|
||||
};
|
||||
|
||||
const requestDifferentialExpression = (set1, set2, num_genes = 50) => async (
|
||||
dispatch,
|
||||
getState
|
||||
) => {
|
||||
dispatch({ type: "request differential expression started" });
|
||||
try {
|
||||
/*
|
||||
Steps:
|
||||
1. get the most differentially expressed genes
|
||||
2. get expression data for each
|
||||
*/
|
||||
const { annoMatrix } = getState();
|
||||
const varIndexName = annoMatrix.schema.annotations.var.index;
|
||||
|
||||
// Legal values are null, Array or TypedArray. Null is initial state.
|
||||
if (!set1) set1 = [];
|
||||
if (!set2) set2 = [];
|
||||
|
||||
// These lines ensure that we convert any TypedArray to an Array.
|
||||
// This is necessary because JSON.stringify() does some very strange
|
||||
// things with TypedArrays (they are marshalled to JSON objects, rather
|
||||
// than being marshalled as a JSON array).
|
||||
set1 = Array.isArray(set1) ? set1 : Array.from(set1);
|
||||
set2 = Array.isArray(set2) ? set2 : Array.from(set2);
|
||||
|
||||
const res = await fetch(
|
||||
`${globals.API.prefix}${globals.API.version}diffexp/obs`,
|
||||
{
|
||||
method: "POST",
|
||||
headers: new Headers({
|
||||
Accept: "application/json",
|
||||
"Content-Type": "application/json",
|
||||
}),
|
||||
body: JSON.stringify({
|
||||
mode: "topN",
|
||||
count: num_genes,
|
||||
set1: { filter: { obs: { index: set1 } } },
|
||||
set2: { filter: { obs: { index: set2 } } },
|
||||
}),
|
||||
credentials: "include",
|
||||
}
|
||||
);
|
||||
|
||||
if (!res.ok || res.headers.get("Content-Type") !== "application/json") {
|
||||
return dispatchDiffExpErrors(dispatch, res);
|
||||
}
|
||||
|
||||
const response = await res.json();
|
||||
const varIndex = await annoMatrix.fetch("var", varIndexName);
|
||||
const diffexpLists = { negative: [], positive: [] };
|
||||
for (const polarity of Object.keys(diffexpLists)) {
|
||||
diffexpLists[polarity] = response[polarity].map((v) => [
|
||||
varIndex.at(v[0], varIndexName),
|
||||
...v.slice(1),
|
||||
]);
|
||||
}
|
||||
|
||||
/* then send the success case action through */
|
||||
return dispatch({
|
||||
type: "request differential expression success",
|
||||
data: diffexpLists,
|
||||
});
|
||||
} catch (error) {
|
||||
return dispatch({
|
||||
type: "request differential expression error",
|
||||
error,
|
||||
});
|
||||
}
|
||||
};
|
||||
|
||||
function fetchJson(pathAndQuery) {
|
||||
return doJsonRequest(
|
||||
`${globals.API.prefix}${globals.API.version}${pathAndQuery}`
|
||||
);
|
||||
}
|
||||
|
||||
export default {
|
||||
doInitialDataLoad,
|
||||
requestDifferentialExpression,
|
||||
requestSingleGeneExpressionCountsForColoringPOST,
|
||||
requestUserDefinedGene,
|
||||
selectContinuousMetadataAction: selnActions.selectContinuousMetadataAction,
|
||||
selectCategoricalMetadataAction: selnActions.selectCategoricalMetadataAction,
|
||||
selectCategoricalAllMetadataAction:
|
||||
selnActions.selectCategoricalAllMetadataAction,
|
||||
graphBrushStartAction: selnActions.graphBrushStartAction,
|
||||
graphBrushChangeAction: selnActions.graphBrushChangeAction,
|
||||
graphBrushDeselectAction: selnActions.graphBrushDeselectAction,
|
||||
graphBrushCancelAction: selnActions.graphBrushCancelAction,
|
||||
graphBrushEndAction: selnActions.graphBrushEndAction,
|
||||
graphLassoStartAction: selnActions.graphLassoStartAction,
|
||||
graphLassoEndAction: selnActions.graphLassoEndAction,
|
||||
graphLassoCancelAction: selnActions.graphLassoCancelAction,
|
||||
graphLassoDeselectAction: selnActions.graphLassoDeselectAction,
|
||||
clipAction: viewActions.clipAction,
|
||||
subsetAction: viewActions.subsetAction,
|
||||
resetSubsetAction: viewActions.resetSubsetAction,
|
||||
annotationCreateCategoryAction: annoActions.annotationCreateCategoryAction,
|
||||
annotationRenameCategoryAction: annoActions.annotationRenameCategoryAction,
|
||||
annotationDeleteCategoryAction: annoActions.annotationDeleteCategoryAction,
|
||||
annotationCreateLabelInCategory: annoActions.annotationCreateLabelInCategory,
|
||||
annotationDeleteLabelFromCategory:
|
||||
annoActions.annotationDeleteLabelFromCategory,
|
||||
annotationRenameLabelInCategory: annoActions.annotationRenameLabelInCategory,
|
||||
annotationLabelCurrentSelection: annoActions.annotationLabelCurrentSelection,
|
||||
saveObsAnnotationsAction: annoActions.saveObsAnnotationsAction,
|
||||
saveGenesetsAction: annoActions.saveGenesetsAction,
|
||||
needToSaveObsAnnotations: annoActions.needToSaveObsAnnotations,
|
||||
layoutChoiceAction: embActions.layoutChoiceAction,
|
||||
setCellSetFromSelection: selnActions.setCellSetFromSelection,
|
||||
genesetDelete: genesetActions.genesetDelete,
|
||||
genesetAddGenes: genesetActions.genesetAddGenes,
|
||||
genesetDeleteGenes: genesetActions.genesetDeleteGenes,
|
||||
};
|
||||
Reference in New Issue
Block a user