mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-10-04 01:18:12 +08:00
Redux refactor (#1571)
* refactor categorical controls state * lint * fix race condition in tests * fix typo * add missing update on subset * remove obsolete code * update jest and puppeteer major version; update all minors * update when label changes * remove lint from tests; increase timeouts in e2e tests * initial refactoring to new async annomatrix * refine error handling * fix bad merge * add continuous legend * lint * fix memoization in color table creators * partial implementation of user defined annotations * add new annotations action creator file * first pass at user annotations * additional user annotation bug fixes * user annotation auto-save * unit test cleanup * lint * refactor into multiple files * cleanup * add column GC * fix several bugs in user annotations * remove debug code * no anonymous functions * undo redo cleanup * file cleanup * scatterplot * performance * cleanup * remove old code * render in parallel with load * fix race condition * simply graph rendering * render throttle DRY * fix category label order * fix typo in e2e test setup * re-fix the e2e test setup * be more tolerant of races * anno matrix unit tests * temp disable reembedding * pilot port continuous histo to react-async * name change * lint * fix repaint bug * typo fix * update snap to match new ids * world/universe name cleanup * move annoMatrix to src dir * use private underscore naming convention * fix corner case in all selected * name cleanup * add layout control * init edge case * lint * port scatterplot * fix label indexing bug and improve tests * port category to react-async * fix user annotation labelling while subset * select all of prev layout on layout switch * fix race with crossfilter update * prettier lint * fix misleading comment * fix url composition in loader * first pass at crossfilter tests * lint * lint * fix typo * improved error handling for network errors * fix memoization bug * add memo * refactor for performnce * add missing single-value handling in select exact parser * small bugs discovered by tests * lint * additional crossfilter unit tests * remove extraneous comment * add support for automatic category determination * lint * fix render bug in category * take advantage of schema categories guarantee * lint * do not clear history when resetting * enhanced annomatrix gc * lint * finish renaming to follow conventions; fix clone race bug * lint * add priority based loading to improve initial data load UX * crossfilter cache perf * perf tuning * remove timers * documentation * PR review changes * PR review changes * more PR review edits * improve clarity of comment * more PR review fixes * port centroidLabels to use react-async * remove dead code * pr review updates * oops, remove logging
This commit is contained in:
Bruce Martin
@@ -0,0 +1,374 @@
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/*
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Action creators for user annotation
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*/
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import _ from "lodash";
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import * as globals from "../globals";
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import { MatrixFBS, AnnotationsHelpers } from "../util/stateManager";
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const { isUserAnnotation } = AnnotationsHelpers;
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export const annotationCreateCategoryAction = (
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newCategoryName,
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categoryToDuplicate
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) => async (dispatch, getState) => {
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/*
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Add a new user-created category to the obs annotations.
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Arguments:
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newCategoryName - string name for the category.
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categoryToDuplicate - obs category to use for initial values, or null.
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*/
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const {
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annoMatrix: prevAnnoMatrix,
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obsCrossfilter: prevObsCrossfilter,
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} = getState();
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if (!prevAnnoMatrix || !prevObsCrossfilter) return;
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const { schema } = prevAnnoMatrix;
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/* name must be a string, non-zero length */
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if (typeof newCategoryName !== "string" || newCategoryName.length === 0)
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throw new Error("user annotations require string name");
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/* ensure the name isn't already in use! */
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if (schema.annotations.obsByName[newCategoryName])
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throw new Error("name collision on annotation category create");
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let initialValue;
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let categories;
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if (categoryToDuplicate) {
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/* if we are duplicating a category, retrieve it */
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const catDupSchema = schema.annotations.obsByName[categoryToDuplicate];
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const catDupType = catDupSchema?.type;
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if (catDupType !== "string" && catDupType !== "categorical")
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throw new Error("categoryToDuplicate does not exist or has invalid type");
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const catToDupDf = await prevAnnoMatrix
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.base()
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.fetch("obs", categoryToDuplicate);
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const col = catToDupDf.col(categoryToDuplicate);
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initialValue = col.asArray();
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({ categories } = col.summarize());
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} else {
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/* else assign to the standard default value */
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initialValue = globals.unassignedCategoryLabel;
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categories = [globals.unassignedCategoryLabel];
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}
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const obsCrossfilter = prevObsCrossfilter.addObsColumn(
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{
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name: newCategoryName,
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type: "categorical",
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categories,
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writable: true,
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},
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Array,
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initialValue
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);
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dispatch({
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type: "annotation: create category",
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data: newCategoryName,
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categoryToDuplicate,
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annoMatrix: obsCrossfilter.annoMatrix,
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obsCrossfilter,
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});
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};
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export const annotationRenameCategoryAction = (
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oldCategoryName,
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newCategoryName
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) => (dispatch, getState) => {
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/*
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Rename a user-created annotation category
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*/
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const {
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annoMatrix: prevAnnoMatrix,
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obsCrossfilter: prevObsCrossfilter,
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} = getState();
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if (!prevAnnoMatrix || !prevObsCrossfilter) return;
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if (!isUserAnnotation(prevAnnoMatrix, oldCategoryName))
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throw new Error("not a user annotation");
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/* name must be a string, non-zero length */
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if (typeof newCategoryName !== "string" || newCategoryName.length === 0)
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throw new Error("user annotations require string name");
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if (oldCategoryName === newCategoryName) return;
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const obsCrossfilter = prevObsCrossfilter.renameObsColumn(
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oldCategoryName,
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newCategoryName
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);
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dispatch({
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type: "annotation: category edited",
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annoMatrix: obsCrossfilter.annoMatrix,
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obsCrossfilter,
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metadataField: oldCategoryName,
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newCategoryText: newCategoryName,
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data: newCategoryName,
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});
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};
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export const annotationDeleteCategoryAction = (categoryName) => (
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dispatch,
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getState
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) => {
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/*
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Delete a user-created category
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*/
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const {
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annoMatrix: prevAnnoMatrix,
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obsCrossfilter: prevObsCrossfilter,
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} = getState();
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if (!prevAnnoMatrix || !prevObsCrossfilter) return;
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if (!isUserAnnotation(prevAnnoMatrix, categoryName))
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throw new Error("not a user annotation");
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const obsCrossfilter = prevObsCrossfilter.dropObsColumn(categoryName);
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dispatch({
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type: "annotation: delete category",
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annoMatrix: obsCrossfilter.annoMatrix,
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obsCrossfilter,
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metadataField: categoryName,
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});
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};
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export const annotationCreateLabelInCategory = (
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categoryName,
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labelName,
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assignSelected
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) => async (dispatch, getState) => {
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/*
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Add a new label to a user-defined category. If assignSelected is true, assign
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the label to all currently selected cells.
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*/
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const {
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annoMatrix: prevAnnoMatrix,
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obsCrossfilter: prevObsCrossfilter,
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} = getState();
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if (!prevAnnoMatrix || !prevObsCrossfilter) return;
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if (!isUserAnnotation(prevAnnoMatrix, categoryName))
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throw new Error("not a user annotation");
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let obsCrossfilter = prevObsCrossfilter.addObsAnnoCategory(
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categoryName,
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labelName
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);
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if (assignSelected) {
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obsCrossfilter = await obsCrossfilter.setObsColumnValues(
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categoryName,
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prevObsCrossfilter.allSelectedLabels(),
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labelName
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);
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}
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dispatch({
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type: "annotation: add new label to category",
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annoMatrix: obsCrossfilter.annoMatrix,
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obsCrossfilter,
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metadataField: categoryName,
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newLabelText: labelName,
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assignSelectedCells: assignSelected,
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});
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};
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export const annotationDeleteLabelFromCategory = (
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categoryName,
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labelName
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) => async (dispatch, getState) => {
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/*
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delete a label from a user-defined category
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*/
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const {
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annoMatrix: prevAnnoMatrix,
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obsCrossfilter: prevObsCrossfilter,
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} = getState();
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if (!prevAnnoMatrix || !prevObsCrossfilter) return;
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if (!isUserAnnotation(prevAnnoMatrix, categoryName))
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throw new Error("not a user annotation");
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const obsCrossfilter = await prevObsCrossfilter.removeObsAnnoCategory(
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categoryName,
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labelName,
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globals.unassignedCategoryLabel
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);
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dispatch({
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type: "annotation: delete label",
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metadataField: categoryName,
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label: labelName,
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annoMatrix: obsCrossfilter.annoMatrix,
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obsCrossfilter,
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});
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};
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export const annotationRenameLabelInCategory = (
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categoryName,
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oldLabelName,
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newLabelName
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) => async (dispatch, getState) => {
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/*
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label name change
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*/
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const {
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annoMatrix: prevAnnoMatrix,
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obsCrossfilter: prevObsCrossfilter,
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} = getState();
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if (!prevAnnoMatrix || !prevObsCrossfilter) return;
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if (!isUserAnnotation(prevAnnoMatrix, categoryName))
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throw new Error("not a user annotation");
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let obsCrossfilter = await prevObsCrossfilter.resetObsColumnValues(
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categoryName,
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oldLabelName,
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newLabelName
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);
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obsCrossfilter = await obsCrossfilter.removeObsAnnoCategory(
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categoryName,
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oldLabelName,
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globals.unassignedCategoryLabel
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);
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dispatch({
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type: "annotation: label edited",
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editedLabel: newLabelName,
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metadataField: categoryName,
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label: oldLabelName,
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annoMatrix: obsCrossfilter.annoMatrix,
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obsCrossfilter,
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});
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};
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export const annotationLabelCurrentSelection = (
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categoryName,
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labelName
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) => async (dispatch, getState) => {
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/*
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set the label on all currently selected
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*/
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const {
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annoMatrix: prevAnnoMatrix,
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obsCrossfilter: prevObsCrossfilter,
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} = getState();
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if (!prevAnnoMatrix || !prevObsCrossfilter) return;
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if (!isUserAnnotation(prevAnnoMatrix, categoryName))
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throw new Error("not a user annotation");
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const obsCrossfilter = await prevObsCrossfilter.setObsColumnValues(
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categoryName,
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prevObsCrossfilter.allSelectedLabels(),
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labelName
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);
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dispatch({
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type: "annotation: label current cell selection",
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metadataField: categoryName,
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label: labelName,
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obsCrossfilter,
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annoMatrix: obsCrossfilter.annoMatrix,
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});
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};
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function writableAnnotations(annoMatrix) {
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return annoMatrix.schema.annotations.obs.columns
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.filter((s) => s.writable)
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.map((s) => s.name);
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}
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export const needToSaveObsAnnotations = (annoMatrix, lastSavedAnnoMatrix) => {
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/*
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Return true if there are LIKELY user-defined annotation modifications between the two
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annoMatrices. Technically not an action creator, but intimately intertwined
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with the save process.
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Two conditions will trigger a need to save:
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* the collection of user-defined columns have changed
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* the contents of the user-defined columns have change
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*/
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annoMatrix = annoMatrix.base();
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// if the annoMatrix hasn't changed, we are guaranteed no changes to the matrix schema or contents.
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if (annoMatrix === lastSavedAnnoMatrix) return false;
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// if the schema has changed, we need to save
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const currentWritable = writableAnnotations(annoMatrix);
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if (_.difference(currentWritable, writableAnnotations(lastSavedAnnoMatrix))) {
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return true;
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}
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// no schema changes; check for change in contents
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return currentWritable.some(
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(col) => annoMatrix.col(col) !== lastSavedAnnoMatrix.col(col)
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);
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};
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export const saveObsAnnotationsAction = () => async (dispatch, getState) => {
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/*
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Save the user-created obs annotations IF any have changed.
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*/
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const state = getState();
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const { annotations, autosave } = state;
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const { dataCollectionNameIsReadOnly, dataCollectionName } = annotations;
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const { lastSavedAnnoMatrix, saveInProgress } = autosave;
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const annoMatrix = state.annoMatrix.base();
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if (saveInProgress || annoMatrix === lastSavedAnnoMatrix) return;
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if (!needToSaveObsAnnotations(annoMatrix, lastSavedAnnoMatrix)) {
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dispatch({
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type: "writable obs annotations - save complete",
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lastSavedAnnoMatrix: annoMatrix,
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});
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return;
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}
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/*
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Else, we really do need to save
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*/
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dispatch({
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type: "writable obs annotations - save started",
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});
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const df = await annoMatrix.fetch("obs", writableAnnotations(annoMatrix));
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const matrix = MatrixFBS.encodeMatrixFBS(df);
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try {
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const queryString =
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!dataCollectionNameIsReadOnly && !!dataCollectionName
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? `?annotation-collection-name=${encodeURIComponent(
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dataCollectionName
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)}`
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: "";
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const res = await fetch(
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`${globals.API.prefix}${globals.API.version}annotations/obs${queryString}`,
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{
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method: "PUT",
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body: matrix,
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headers: new Headers({
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"Content-Type": "application/octet-stream",
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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) {
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dispatch({
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||||
type: "writable obs annotations - save complete",
|
||||
lastSavedAnnoMatrix: annoMatrix,
|
||||
});
|
||||
} else {
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dispatch({
|
||||
type: "writable obs annotations - save error",
|
||||
message: `HTTP error ${res.status} - ${res.statusText}`,
|
||||
res,
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||||
});
|
||||
}
|
||||
} catch (error) {
|
||||
dispatch({
|
||||
type: "writable obs annotations - save error",
|
||||
message: error.toString(),
|
||||
error,
|
||||
});
|
||||
}
|
||||
};
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+139
-313
@@ -1,93 +1,21 @@
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||||
import * as globals from "../globals";
|
||||
import { Universe, MatrixFBS } from "../util/stateManager";
|
||||
import * as Dataframe from "../util/dataframe";
|
||||
import {
|
||||
AnnoMatrixLoader,
|
||||
AnnoMatrixObsCrossfilter,
|
||||
clip,
|
||||
isubsetMask,
|
||||
} from "../annoMatrix";
|
||||
import {
|
||||
catchErrorsWrap,
|
||||
doJsonRequest,
|
||||
doBinaryRequest,
|
||||
dispatchNetworkErrorMessageToUser,
|
||||
} from "../util/actionHelpers";
|
||||
import PromiseLimit from "../util/promiseLimit";
|
||||
import { requestReembed, reembedResetWorldToUniverse } from "./reembed";
|
||||
import {
|
||||
requestReembed /* , reembedResetWorldToUniverse -- disabled temporarily, TODO issue #1606 */,
|
||||
} from "./reembed";
|
||||
import { loadUserColorConfig } from "../util/stateManager/colorHelpers";
|
||||
|
||||
/*
|
||||
return promise to fetch the OBS annotations we need to load. Omit anything
|
||||
we don't need.
|
||||
*/
|
||||
async function obsAnnotationFetchAndLoad(dispatch, schema) {
|
||||
const obsAnnotations = schema?.schema?.annotations?.obs ?? {};
|
||||
const index = obsAnnotations.index ?? false;
|
||||
const columns = (obsAnnotations.columns ?? []).filter(
|
||||
(col) => col.name !== index
|
||||
);
|
||||
|
||||
const plimit = new PromiseLimit(5);
|
||||
return Promise.all(
|
||||
columns.map((col) =>
|
||||
plimit.add(() =>
|
||||
fetchBinary(
|
||||
`annotations/obs?annotation-name=${encodeURIComponent(col.name)}`
|
||||
)
|
||||
.then((buffer) => MatrixFBS.matrixFBSToDataframe(buffer))
|
||||
.then((df) =>
|
||||
dispatch({
|
||||
type: "universe: column load success",
|
||||
dim: "obsAnnotations",
|
||||
dataframe: df,
|
||||
})
|
||||
)
|
||||
)
|
||||
)
|
||||
);
|
||||
}
|
||||
|
||||
/*
|
||||
return promise fetching VAR annotations we need to load. Only index is currently used.
|
||||
*/
|
||||
async function varAnnotationFetchAndLoad(dispatch, schema) {
|
||||
const varAnnotations = schema?.schema?.annotations?.var ?? {};
|
||||
const index = varAnnotations.index ?? false;
|
||||
const names = index ? [index] : [];
|
||||
return Promise.all(
|
||||
names.map((name) =>
|
||||
fetchBinary(`annotations/var?annotation-name=${encodeURIComponent(name)}`)
|
||||
.then((buffer) => MatrixFBS.matrixFBSToDataframe(buffer))
|
||||
.then((df) =>
|
||||
dispatch({
|
||||
type: "universe: column load success",
|
||||
dim: "varAnnotations",
|
||||
dataframe: df,
|
||||
})
|
||||
)
|
||||
)
|
||||
);
|
||||
}
|
||||
|
||||
/*
|
||||
return promise fetching layout we need
|
||||
*/
|
||||
function layoutFetchAndLoad(dispatch, schema) {
|
||||
const embeddings = schema?.schema?.layout?.obs ?? [];
|
||||
const embNames = embeddings.map((e) => e.name);
|
||||
|
||||
const plimit = new PromiseLimit(5);
|
||||
return Promise.all(
|
||||
embNames.map((e) =>
|
||||
plimit.add(() =>
|
||||
fetchBinary(
|
||||
`layout/obs?layout-name=${encodeURIComponent(e)}`
|
||||
).then((buffer) => MatrixFBS.matrixFBSToDataframe(buffer))
|
||||
)
|
||||
)
|
||||
).then((dfs) =>
|
||||
dispatch({
|
||||
type: "universe: column load success",
|
||||
dim: "obsLayout",
|
||||
dataframe: Dataframe.Dataframe.empty().withColsFromAll(dfs),
|
||||
})
|
||||
);
|
||||
}
|
||||
import * as selnActions from "./selection";
|
||||
import * as annoActions from "./annotation";
|
||||
|
||||
/*
|
||||
return promise fetching user-configured colors
|
||||
@@ -101,178 +29,62 @@ async function userColorsFetchAndLoad(dispatch) {
|
||||
);
|
||||
}
|
||||
|
||||
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;
|
||||
});
|
||||
}
|
||||
|
||||
/*
|
||||
Bootstrap application with the initial data loading.
|
||||
* /config - application configuration
|
||||
* /schema - schema of dataframe
|
||||
* /annotations - all metadata annotation
|
||||
* /layout - all default layout
|
||||
Application bootstrap
|
||||
*/
|
||||
const doInitialDataLoad = () =>
|
||||
catchErrorsWrap(async (dispatch) => {
|
||||
dispatch({ type: "initial data load start" });
|
||||
|
||||
try {
|
||||
/*
|
||||
Step 1 - config & schema, all JSON
|
||||
*/
|
||||
const requestJson = ["config", "schema"].map(fetchJson);
|
||||
const [responseConfig, schema] = await Promise.all(requestJson);
|
||||
/* set config defaults */
|
||||
const config = { ...globals.configDefaults, ...responseConfig.config };
|
||||
const universe = Universe.createUniverseFromResponse(config, schema);
|
||||
dispatch({
|
||||
type: "universe exists, but loading is still in progress",
|
||||
universe,
|
||||
});
|
||||
dispatch({
|
||||
type: "configuration load complete",
|
||||
config,
|
||||
});
|
||||
|
||||
/*
|
||||
Step 2 - load the minimum stuff required to display.
|
||||
*/
|
||||
await Promise.all([
|
||||
const [, schema] = await Promise.all([
|
||||
configFetch(dispatch),
|
||||
schemaFetch(dispatch),
|
||||
userColorsFetchAndLoad(dispatch),
|
||||
layoutFetchAndLoad(dispatch, schema),
|
||||
varAnnotationFetchAndLoad(dispatch, schema),
|
||||
]);
|
||||
|
||||
/*
|
||||
Step 3 - load everything else
|
||||
*/
|
||||
await obsAnnotationFetchAndLoad(dispatch, schema);
|
||||
|
||||
const baseDataUrl = `${globals.API.prefix}${globals.API.version}`;
|
||||
const annoMatrix = new AnnoMatrixLoader(baseDataUrl, schema.schema);
|
||||
const obsCrossfilter = new AnnoMatrixObsCrossfilter(annoMatrix);
|
||||
dispatch({
|
||||
type: "initial data load complete (universe exists)",
|
||||
universe,
|
||||
type: "annoMatrix: init complete",
|
||||
annoMatrix,
|
||||
obsCrossfilter,
|
||||
});
|
||||
dispatch({ type: "initial data load complete" });
|
||||
} catch (error) {
|
||||
dispatch({ type: "initial data load error", error });
|
||||
}
|
||||
}, true);
|
||||
|
||||
/*
|
||||
Set the view (world) to current selection. Placeholder for an async action
|
||||
which also does re-layout.
|
||||
*/
|
||||
const setWorldToSelection = () => (dispatch, getState) => {
|
||||
const { universe, world, crossfilter } = getState();
|
||||
dispatch({
|
||||
type: "set World to current selection",
|
||||
universe,
|
||||
world,
|
||||
crossfilter,
|
||||
});
|
||||
};
|
||||
|
||||
/* double URI encode - needed for query-param filters */
|
||||
function dubEncURIComponent(s) {
|
||||
return encodeURIComponent(encodeURIComponent(s));
|
||||
}
|
||||
|
||||
/*
|
||||
Fetch expression vectors for each gene in genes. This is NOT an action
|
||||
function, but rather a helper to be called from an action helper that
|
||||
needs expression data.
|
||||
|
||||
Transparently utilizes cached data if it is already present.
|
||||
*/
|
||||
async function _doRequestExpressionData(dispatch, getState, genes) {
|
||||
const state = getState();
|
||||
const { universe } = state;
|
||||
const varIndexName = universe.schema.annotations.var.index;
|
||||
|
||||
/* helper for this function only */
|
||||
const fetchData = async (geneNames) => {
|
||||
const query = geneNames
|
||||
.map(
|
||||
(g) =>
|
||||
`var:${dubEncURIComponent(varIndexName)}=${dubEncURIComponent(g)}`
|
||||
)
|
||||
.join("&");
|
||||
// TODO: why convert to an Object and not a Dataframe?
|
||||
return fetchBinary(`data/var?${query}`).then((buffer) =>
|
||||
Universe.convertDataFBStoObject(universe, buffer)
|
||||
);
|
||||
};
|
||||
|
||||
/* preload data already in cache */
|
||||
let expressionData = genes.reduce((acc, g) => {
|
||||
const data = universe.varData.col(g);
|
||||
if (data) {
|
||||
acc[g] = data.asArray();
|
||||
}
|
||||
return acc;
|
||||
}, {}); // --> { gene: data }
|
||||
|
||||
/* make a list of genes for which we do not have data */
|
||||
const genesToFetch = genes.filter((g) => expressionData[g] === undefined);
|
||||
|
||||
dispatch({ type: "expression load start" });
|
||||
|
||||
/* Fetch data for any genes not in cache */
|
||||
if (genesToFetch.length) {
|
||||
try {
|
||||
const newExpressionData = await fetchData(genesToFetch);
|
||||
expressionData = {
|
||||
...expressionData,
|
||||
...newExpressionData,
|
||||
};
|
||||
} catch (error) {
|
||||
dispatch({ type: "expression load error", error });
|
||||
throw error; // rethrow
|
||||
}
|
||||
}
|
||||
|
||||
dispatch({ type: "expression load success", expressionData });
|
||||
return expressionData;
|
||||
}
|
||||
|
||||
function requestSingleGeneExpressionCountsForColoringPOST(gene) {
|
||||
return async (dispatch, getState) => {
|
||||
dispatch({ type: "get single gene expression for coloring started" });
|
||||
try {
|
||||
await _doRequestExpressionData(dispatch, getState, [gene]);
|
||||
const { world } = getState();
|
||||
dispatch({
|
||||
type: "color by expression",
|
||||
gene,
|
||||
data: {
|
||||
[gene]: world.varData.col(gene).asArray(),
|
||||
},
|
||||
});
|
||||
} catch (error) {
|
||||
dispatch({
|
||||
type: "get single gene expression for coloring error",
|
||||
error,
|
||||
});
|
||||
}
|
||||
return {
|
||||
type: "color by expression",
|
||||
gene,
|
||||
};
|
||||
}
|
||||
|
||||
const requestUserDefinedGene = (gene) => async (dispatch, getState) => {
|
||||
dispatch({ type: "request user defined gene started" });
|
||||
try {
|
||||
await await _doRequestExpressionData(dispatch, getState, [gene]);
|
||||
const { world } = getState();
|
||||
|
||||
/* then send the success case action through */
|
||||
return dispatch({
|
||||
type: "request user defined gene success",
|
||||
data: {
|
||||
genes: [gene],
|
||||
expression: world.varData.col(gene).asArray(),
|
||||
},
|
||||
});
|
||||
} catch (error) {
|
||||
return dispatch({
|
||||
type: "request user defined gene error",
|
||||
error,
|
||||
});
|
||||
}
|
||||
};
|
||||
const requestUserDefinedGene = (gene) => ({
|
||||
type: "request user defined gene success",
|
||||
data: {
|
||||
genes: [gene],
|
||||
},
|
||||
});
|
||||
|
||||
const dispatchDiffExpErrors = (dispatch, response) => {
|
||||
switch (response.status) {
|
||||
@@ -308,9 +120,8 @@ const requestDifferentialExpression = (set1, set2, num_genes = 10) => async (
|
||||
1. get the most differentially expressed genes
|
||||
2. get expression data for each
|
||||
*/
|
||||
const state = getState();
|
||||
const { universe } = state;
|
||||
const varIndexName = universe.schema.annotations.var.index;
|
||||
const { annoMatrix } = getState();
|
||||
const varIndexName = annoMatrix.schema.annotations.var.index;
|
||||
|
||||
// Legal values are null, Array or TypedArray. Null is initial state.
|
||||
if (!set1) set1 = [];
|
||||
@@ -345,22 +156,12 @@ const requestDifferentialExpression = (set1, set2, num_genes = 10) => async (
|
||||
return dispatchDiffExpErrors(dispatch, res);
|
||||
}
|
||||
|
||||
const data = await res.json();
|
||||
// result is [ [varIdx, ...], ... ]
|
||||
const topNGenes = data.map((r) =>
|
||||
universe.varAnnotations.at(r[0], varIndexName)
|
||||
);
|
||||
|
||||
/*
|
||||
Kick off secondary action to fetch all of the expression data for the
|
||||
topN expressed genes.
|
||||
*/
|
||||
const plimit = new PromiseLimit(5);
|
||||
await Promise.all(
|
||||
topNGenes.map((gene) =>
|
||||
plimit.add(() => _doRequestExpressionData(dispatch, getState, [gene]))
|
||||
)
|
||||
);
|
||||
const response = await res.json();
|
||||
const varIndex = await annoMatrix.fetch("var", varIndexName);
|
||||
const data = response.map((v) => [
|
||||
varIndex.at(v[0], varIndexName),
|
||||
...v.slice(1),
|
||||
]);
|
||||
|
||||
/* then send the success case action through */
|
||||
return dispatch({
|
||||
@@ -375,66 +176,73 @@ const requestDifferentialExpression = (set1, set2, num_genes = 10) => async (
|
||||
}
|
||||
};
|
||||
|
||||
const resetWorldToUniverse = () => (dispatch, getState) => {
|
||||
const { universe } = getState();
|
||||
reembedResetWorldToUniverse(dispatch, getState);
|
||||
const clipAction = (min, max) => (dispatch, getState) => {
|
||||
/*
|
||||
apply a clip to the current annoMatrix. By convention, the clip
|
||||
view is ALWAYS the top view.
|
||||
*/
|
||||
const { annoMatrix: prevAnnoMatrix } = getState();
|
||||
const annoMatrix = prevAnnoMatrix.isClipped
|
||||
? clip(prevAnnoMatrix.viewOf, min, max)
|
||||
: clip(prevAnnoMatrix, min, max);
|
||||
const obsCrossfilter = new AnnoMatrixObsCrossfilter(annoMatrix);
|
||||
dispatch({
|
||||
type: "reset World to eq Universe",
|
||||
universe,
|
||||
type: "set clip quantiles",
|
||||
clipQuantiles: { min, max },
|
||||
annoMatrix,
|
||||
obsCrossfilter,
|
||||
});
|
||||
};
|
||||
|
||||
const saveObsAnnotations = () => async (dispatch, getState) => {
|
||||
const { universe, annotations } = getState();
|
||||
const { obsAnnotations, schema } = universe;
|
||||
const { dataCollectionNameIsReadOnly, dataCollectionName } = annotations;
|
||||
const subsetAction = () => (dispatch, getState) => {
|
||||
/*
|
||||
Subset the annoMatrix to the current crossfilter selection
|
||||
*/
|
||||
const {
|
||||
annoMatrix: prevAnnoMatrix,
|
||||
obsCrossfilter: prevObsCrossfilter,
|
||||
} = getState();
|
||||
|
||||
const annoMatrix = isubsetMask(
|
||||
prevAnnoMatrix,
|
||||
prevObsCrossfilter.allSelectedMask()
|
||||
);
|
||||
const obsCrossfilter = new AnnoMatrixObsCrossfilter(annoMatrix);
|
||||
dispatch({
|
||||
type: "writable obs annotations - save started",
|
||||
type: "subset to selection",
|
||||
annoMatrix,
|
||||
obsCrossfilter,
|
||||
});
|
||||
};
|
||||
|
||||
const writableAnnotations = schema.annotations.obs.columns
|
||||
.filter((s) => s.writable)
|
||||
.map((s) => s.name);
|
||||
const df = obsAnnotations.subset(null, writableAnnotations);
|
||||
const matrix = MatrixFBS.encodeMatrixFBS(df);
|
||||
try {
|
||||
const queryString =
|
||||
!dataCollectionNameIsReadOnly && !!dataCollectionName
|
||||
? `?annotation-collection-name=${encodeURIComponent(
|
||||
dataCollectionName
|
||||
)}`
|
||||
: "";
|
||||
const res = await fetch(
|
||||
`${globals.API.prefix}${globals.API.version}annotations/obs${queryString}`,
|
||||
{
|
||||
method: "PUT",
|
||||
body: matrix,
|
||||
headers: new Headers({
|
||||
"Content-Type": "application/octet-stream",
|
||||
}),
|
||||
credentials: "include",
|
||||
}
|
||||
);
|
||||
if (res.ok) {
|
||||
dispatch({
|
||||
type: "writable obs annotations - save complete",
|
||||
obsAnnotations,
|
||||
});
|
||||
} else {
|
||||
dispatch({
|
||||
type: "writable obs annotations - save error",
|
||||
message: `HTTP error ${res.status} - ${res.statusText}`,
|
||||
res,
|
||||
});
|
||||
}
|
||||
} catch (error) {
|
||||
dispatch({
|
||||
type: "writable obs annotations - save error",
|
||||
message: error.toString(),
|
||||
error,
|
||||
});
|
||||
const resetSubsetAction = () => (dispatch, getState) => {
|
||||
/*
|
||||
Reset the annoMatrix to all data. Because we may have multiple views
|
||||
stacked, we pop them all. By convention, any clip transformation will
|
||||
be the top of the stack, and must be preserved.
|
||||
*/
|
||||
|
||||
const { annoMatrix: prevAnnoMatrix } = getState();
|
||||
|
||||
const clipRange = prevAnnoMatrix.isClipped ? prevAnnoMatrix.clipRange : null;
|
||||
|
||||
/* pop all views */
|
||||
let annoMatrix = prevAnnoMatrix;
|
||||
while (annoMatrix.isView) {
|
||||
annoMatrix = annoMatrix.viewOf;
|
||||
}
|
||||
|
||||
/* re-apply the clip, if any */
|
||||
if (clipRange !== null) {
|
||||
annoMatrix = clip(annoMatrix, ...clipRange);
|
||||
}
|
||||
|
||||
const obsCrossfilter = new AnnoMatrixObsCrossfilter(annoMatrix);
|
||||
dispatch({
|
||||
type: "reset subset",
|
||||
annoMatrix,
|
||||
obsCrossfilter,
|
||||
});
|
||||
};
|
||||
|
||||
function fetchJson(pathAndQuery) {
|
||||
@@ -443,19 +251,37 @@ function fetchJson(pathAndQuery) {
|
||||
);
|
||||
}
|
||||
|
||||
function fetchBinary(pathAndQuery) {
|
||||
return doBinaryRequest(
|
||||
`${globals.API.prefix}${globals.API.version}${pathAndQuery}`
|
||||
);
|
||||
}
|
||||
|
||||
export default {
|
||||
doInitialDataLoad,
|
||||
requestDifferentialExpression,
|
||||
requestSingleGeneExpressionCountsForColoringPOST,
|
||||
requestUserDefinedGene,
|
||||
requestReembed,
|
||||
resetWorldToUniverse,
|
||||
saveObsAnnotations,
|
||||
setWorldToSelection,
|
||||
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,
|
||||
subsetAction,
|
||||
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,
|
||||
needToSaveObsAnnotations: annoActions.needToSaveObsAnnotations,
|
||||
layoutChoiceAction: selnActions.layoutChoiceAction,
|
||||
};
|
||||
|
||||
@@ -104,6 +104,7 @@ export function requestReembed() {
|
||||
};
|
||||
}
|
||||
|
||||
/* disabled until reimplementation occurs
|
||||
export function reembedResetWorldToUniverse(dispatch, getState) {
|
||||
const { reembedController } = getState();
|
||||
if (reembedController.pendingFetch) reembedController.pendingFetch.abort();
|
||||
@@ -111,3 +112,4 @@ export function reembedResetWorldToUniverse(dispatch, getState) {
|
||||
type: "reembed: clear all reembeddings",
|
||||
});
|
||||
}
|
||||
*/
|
||||
|
||||
@@ -0,0 +1,211 @@
|
||||
/*
|
||||
Action creators for selection
|
||||
*/
|
||||
export const selectContinuousMetadataAction = (
|
||||
type,
|
||||
query,
|
||||
range,
|
||||
oldProps = {}
|
||||
) => async (dispatch, getState) => {
|
||||
const { obsCrossfilter: prevObsCrossfilter } = getState();
|
||||
|
||||
const selection = range
|
||||
? {
|
||||
mode: "range",
|
||||
lo: range[0],
|
||||
hi: range[1],
|
||||
inclusive: true, // [lo, hi] incluisve selection
|
||||
}
|
||||
: { mode: "all" };
|
||||
|
||||
const obsCrossfilter = await prevObsCrossfilter.select(...query, selection);
|
||||
|
||||
dispatch({
|
||||
type,
|
||||
obsCrossfilter,
|
||||
range,
|
||||
...oldProps,
|
||||
});
|
||||
};
|
||||
|
||||
export const selectCategoricalMetadataAction = (
|
||||
type, // action type
|
||||
metadataField, // annotation category name
|
||||
labels,
|
||||
label, // the label being selected/deselected
|
||||
isSelected, // bool
|
||||
oldProps = {}
|
||||
) => async (dispatch, getState) => {
|
||||
const {
|
||||
obsCrossfilter: prevObsCrossfilter,
|
||||
categoricalSelection,
|
||||
} = getState();
|
||||
|
||||
const labelSelectionState = new Map(categoricalSelection[metadataField]);
|
||||
labels.forEach(
|
||||
(l) => labelSelectionState.has(l) || labelSelectionState.set(l, true)
|
||||
);
|
||||
labelSelectionState.set(label, isSelected);
|
||||
|
||||
const values = Array.from(labelSelectionState.keys()).filter((k) =>
|
||||
labelSelectionState.get(k)
|
||||
);
|
||||
const selection = {
|
||||
mode: "exact",
|
||||
values,
|
||||
};
|
||||
const obsCrossfilter = await prevObsCrossfilter.select(
|
||||
"obs",
|
||||
metadataField,
|
||||
selection
|
||||
);
|
||||
|
||||
dispatch({
|
||||
type,
|
||||
obsCrossfilter,
|
||||
metadataField,
|
||||
labelSelectionState,
|
||||
...oldProps,
|
||||
});
|
||||
};
|
||||
|
||||
export const selectCategoricalAllMetadataAction = (
|
||||
type, // action type
|
||||
metadataField, // annotation category name
|
||||
labels,
|
||||
isSelected, // bool, select all or none
|
||||
oldProps = {}
|
||||
) => async (dispatch, getState) => {
|
||||
const {
|
||||
obsCrossfilter: prevObsCrossfilter,
|
||||
categoricalSelection,
|
||||
} = getState();
|
||||
|
||||
const labelSelectionState = new Map(categoricalSelection[metadataField]);
|
||||
labels.forEach((label) => labelSelectionState.set(label, isSelected));
|
||||
|
||||
const selection = { mode: isSelected ? "all" : "none" };
|
||||
const obsCrossfilter = await prevObsCrossfilter.select(
|
||||
"obs",
|
||||
metadataField,
|
||||
selection
|
||||
);
|
||||
|
||||
dispatch({
|
||||
type,
|
||||
obsCrossfilter,
|
||||
metadataField,
|
||||
labelSelectionState,
|
||||
...oldProps,
|
||||
});
|
||||
};
|
||||
|
||||
/**
|
||||
** Graph selection-related actions
|
||||
**/
|
||||
|
||||
export const graphBrushStartAction = () =>
|
||||
/* no change to crossfilter until a change fires */
|
||||
({ type: "graph brush start" });
|
||||
|
||||
const _graphBrushWithinRectAction = (type, embName, brushCoords) => async (
|
||||
dispatch,
|
||||
getState
|
||||
) => {
|
||||
const { obsCrossfilter: prevObsCrossfilter } = getState();
|
||||
|
||||
const selection = { mode: "within-rect", ...brushCoords };
|
||||
const obsCrossfilter = await prevObsCrossfilter.select(
|
||||
"emb",
|
||||
embName,
|
||||
selection
|
||||
);
|
||||
|
||||
dispatch({
|
||||
type,
|
||||
obsCrossfilter,
|
||||
brushCoords,
|
||||
});
|
||||
};
|
||||
|
||||
const _graphAllAction = (type, embName) => async (dispatch, getState) => {
|
||||
const { obsCrossfilter: prevObsCrossfilter } = getState();
|
||||
|
||||
const obsCrossfilter = await prevObsCrossfilter.select("emb", embName, {
|
||||
mode: "all",
|
||||
});
|
||||
|
||||
dispatch({
|
||||
type,
|
||||
obsCrossfilter,
|
||||
});
|
||||
};
|
||||
|
||||
export const graphBrushChangeAction = (embName, brushCoords) =>
|
||||
_graphBrushWithinRectAction("graph brush change", embName, brushCoords);
|
||||
|
||||
export const graphBrushEndAction = (embName, brushCoords) =>
|
||||
_graphBrushWithinRectAction("graph brush end", embName, brushCoords);
|
||||
|
||||
export const graphBrushCancelAction = (embName) =>
|
||||
_graphAllAction("graph brush cancel", embName);
|
||||
export const graphBrushDeselectAction = (embName) =>
|
||||
_graphAllAction("graph brush deselect", embName);
|
||||
|
||||
export const graphLassoStartAction = () =>
|
||||
/* no change to crossfilter until a change fires */
|
||||
({ type: "graph lasso start" });
|
||||
|
||||
export const graphLassoCancelAction = (embName) =>
|
||||
_graphAllAction("graph lasso cancel", embName);
|
||||
|
||||
export const graphLassoDeselectAction = (embName) =>
|
||||
_graphAllAction("graph lasso cancel", embName);
|
||||
|
||||
export const graphLassoEndAction = (embName, polygon) => async (
|
||||
dispatch,
|
||||
getState
|
||||
) => {
|
||||
const { obsCrossfilter: prevObsCrossfilter } = getState();
|
||||
|
||||
const selection = {
|
||||
mode: "within-polygon",
|
||||
polygon,
|
||||
};
|
||||
const obsCrossfilter = await prevObsCrossfilter.select(
|
||||
"emb",
|
||||
embName,
|
||||
selection
|
||||
);
|
||||
|
||||
dispatch({
|
||||
type: "graph lasso end",
|
||||
obsCrossfilter,
|
||||
polygon,
|
||||
});
|
||||
};
|
||||
|
||||
export const layoutChoiceAction = (newLayoutChoice) => async (
|
||||
dispatch,
|
||||
getState
|
||||
) => {
|
||||
/*
|
||||
On layout choice, make sure we have selected all on the previous layout, AND the new
|
||||
layout.
|
||||
*/
|
||||
const { obsCrossfilter: prevObsCrossfilter, layoutChoice } = getState();
|
||||
|
||||
let obsCrossfilter = await prevObsCrossfilter.select(
|
||||
"emb",
|
||||
layoutChoice.current,
|
||||
{ mode: "all" }
|
||||
);
|
||||
obsCrossfilter = await obsCrossfilter.select("emb", newLayoutChoice, {
|
||||
mode: "all",
|
||||
});
|
||||
dispatch({
|
||||
type: "set layout choice",
|
||||
layoutChoice: newLayoutChoice,
|
||||
obsCrossfilter,
|
||||
});
|
||||
};
|
||||
Reference in New Issue
Block a user