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https://github.com/chanzuckerberg/cellxgene.git
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Experimental - manual annotations (#837)
* icons, partway * redux for values * onChange * cancel * annotations lifecycle for category names * copy categorical * edit category * add Dataframe.withColsFrom * render user annotations; default add/delete annotation category * add label name to actions * category name edit * error checking improvements * change schema field isUserAnnotation to writable * always have an unassigned label; implement delete label * implement add new label and edit label name * label current cell selection * fix select exact bug in crossfilter * clean up categorical reducer * fix tests * remove debugging printf * implement subset/reset for user annotations * undo redo support for user annotations * remove duplicate button from categories * add modal * remove obsolete duplicate annotation reducers * remove old debugging printf * connect modal to annotation create and dup * initial full-stack wiring * finish up end-to-end wiring * fix existing unit tests * fix pytests to match new schema API * remove debugging printfs * add label file rotation * remove obsolete comment * add fbs encode/decode tests * add tests for writable annotations * simplify code * fix hashing bug with FBS encoding * lint * fix smoke tests * improve error checking in Dataframe.withColsFrom * add unit test for Dataframe.withColsFrom * add unit test for Dataframe.columns and Dataframe.renameCol * fix bug in FBS encode, add better error checks, refactor * add FBS encode/decode test * add clarifying comment * clean up action type names; fix state inconsistency in crossfilter update * change autosave timer to 2.5sec * sort categorical metadata render order so it remains consistent * add temporary autogenerated label for add-new-label operation * fix hover-over label menu interference with cell highlighting * remove debugging code * add missing reducer cases & fix typo * make dataframe memoize more general purpose * add dev mode for annos * fix error on select duplicate * handle zero occupancy categories * correctly maintain unclipped AND clipped world * correctly handle zero length FBS matrix and label files * ensure all writable categorical schema contains an unassigned category * handle case where building occupancy stack for category with no members * dialog for creating label, disable button if duplicate or empty * visually separate writeable * edit category * fix edit category name * remove debugging code * fix edit annotation label * visually define unassigned, change options * Pull in requirements.txt from `master` * label currently selected cells * duplicate label * lint * fix pytest merge issues * rename --label-file to --experimental-label-file * remove debugging console log * spelling error fix; fix bug found in PR review. * lint
This commit is contained in:
Bruce Martin
committed by
Colin Megill
Colin Megill
parent
ab2c423006
commit
3660a6cc27
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/*
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Helper functions for user-editable nnotations state management.
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See also reducers/annotations.js
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*/
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import { unassignedCategoryLabel } from "../../globals";
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import * as SchemaHelpers from "./schemaHelpers";
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import { obsAnnoDimensionName } from "../nameCreators";
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/*
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There are a number of state constraints assumed throughout the
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application:
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- all obs annotations are in {world|universe}.obsAnnotations,
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regardless of whether or not they are user editable.
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- the {world|universe}.schema is always up to date and matches
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the data
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- the schema flag `writable` correctly indicates whether
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the annotation is editable/mutable.
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In addition, the current state management only allows for
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categorical annotations to be writable.
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*/
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export function isCategoricalAnnotation(schema, name) {
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/* we treat any string, categorical or boolean as a categorical */
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const { type } = schema.annotations.obsByName[name];
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return type === "string" || type === "boolean" || type === "categorical";
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}
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export function isContinuousAnnotation(schema, name) {
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return !isCategoricalAnnotation(schema, name);
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}
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function _isUserAnnotation(schema, name) {
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return schema.annotations.obsByName[name]?.writable;
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}
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export function isUserAnnotation(worldOrUniverse, name) {
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return _isUserAnnotation(worldOrUniverse.schema, name);
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}
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export function removeObsAnnoSchema(schema, name) {
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/*
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remove named annotation from obs annotation schema
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*/
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/* only remove if it exists and is a user annotation */
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if (!_isUserAnnotation(schema, name))
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throw new Error("removing non-user-defined schema");
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return SchemaHelpers.removeObsAnnoColumn(schema, name);
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}
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export function addObsAnnoSchema(schema, name, colSchema) {
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/*
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add a categorical type to the obs annotation schema
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*/
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/* collision detection */
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if (schema.annotations.obs.columns.some(v => v.name === name))
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throw Error("annotations may not contain duplicate category names");
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if (name !== colSchema.name) throw Error("column schema does not match");
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return SchemaHelpers.addObsAnnoColumn(schema, name, colSchema);
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}
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export function dupObsAnnoSchema(schema, sourceName, dupName, defaultSchema) {
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/*
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duplicate the obs annotation `sourceName` schema, but with the name `dupName`
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*/
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const colSchema = {
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...schema.annotations.obsByName[sourceName],
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...defaultSchema,
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name: dupName
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};
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/* existance check */
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if (!colSchema) throw Error("source annotation does not exist");
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/* collision detection */
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if (schema.annotations.obs.columns.some(v => v.name === dupName))
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throw Error("annotations may not contain duplicate category names");
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return SchemaHelpers.addObsAnnoColumn(schema, dupName, colSchema);
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}
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export function removeObsAnnoCategory(schema, name, category) {
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/* don't allow deletion of unassigned category on writable annotations */
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if (!_isUserAnnotation(schema, name))
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throw new Error("unable to modify read-only schema");
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if (category === unassignedCategoryLabel)
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throw new Error("may not remove unassigned category label");
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return SchemaHelpers.removeObsAnnoCategory(schema, name, category);
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}
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export function addObsAnnoCategory(schema, name, category) {
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if (!_isUserAnnotation(schema, name))
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throw new Error("unable to modify read-only schema");
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return SchemaHelpers.addObsAnnoCategory(schema, name, category);
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}
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export function setLabelByValue(df, colName, fromLabel, toLabel) {
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/*
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in the dataframe column `colName`, set any value of `fromLabel` to `toLabel`
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*/
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const keys = df.colIndex.keys();
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const ndf = df.mapColumns((col, colIdx) => {
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if (colName !== keys[colIdx]) return col;
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/* clone data and return it. */
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const newCol = col.slice();
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for (let i = 0, l = newCol.length; i < l; i += 1) {
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if (newCol[i] === fromLabel) newCol[i] = toLabel;
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}
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return newCol;
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});
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return ndf;
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}
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export function setLabelByMask(df, colName, mask, label) {
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/*
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in the dataframe column `colName`, set the masked rows to 'label'
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*/
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const keys = df.colIndex.keys();
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const ndf = df.mapColumns((col, colIdx) => {
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if (colName !== keys[colIdx]) return col;
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/* clone data and return it. */
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const newCol = col.slice();
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for (let i = 0, l = newCol.length; i < l; i += 1) {
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if (mask[i]) newCol[i] = label;
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}
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return newCol;
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});
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return ndf;
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}
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export function worldToUniverseMask(worldMask, worldObsAnnotations, nObs) {
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/*
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given world seleciton mask, return a selection mask for entire universe
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that has same selection state.
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*/
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const mask = new Uint8Array(nObs);
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const { rowIndex } = worldObsAnnotations;
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for (let i = 0, l = worldMask.length; i < l; i += 1) {
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if (worldMask[i]) {
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const label = rowIndex.getLabel(i);
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mask[label] = 1;
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}
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}
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return mask;
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}
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export function createWritableAnnotationDimensions(world, crossfilter) {
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const { obsAnnotations, schema } = world;
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const writableAnnotations = schema.annotations.obs.columns
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.filter(s => s.writable)
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.map(s => s.name);
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crossfilter = writableAnnotations.reduce((xflt, anno) => {
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const dimName = obsAnnoDimensionName(anno);
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if (xflt.hasDimension(dimName)) xflt = xflt.delDimension(dimName);
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return xflt.addDimension(
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dimName,
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"enum",
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obsAnnotations.col(anno).asArray()
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);
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}, crossfilter);
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return crossfilter;
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}
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