mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-10-05 01:08:11 +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",
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lastSavedAnnoMatrix: annoMatrix,
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});
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} else {
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dispatch({
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type: "writable obs annotations - save error",
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message: `HTTP error ${res.status} - ${res.statusText}`,
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res,
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});
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}
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} catch (error) {
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dispatch({
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type: "writable obs annotations - save error",
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message: error.toString(),
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error,
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});
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}
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};
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