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TS Revert (1) (#2402)
* revert all commits to before Typescript migration * update compat workflow to match latest deps (#2335) * update compat workflow to match latest deps * attempt to debug * attempt to debug * remove debugging code * typo * update deps to match desktop (#2340) * fix: don't run lint with `--fix` on push tests (#2273) * fix: don't run lint with `--fix` on push tests * npx Co-authored-by: maniarathi <mani.arathi@gmail.com> Co-authored-by: Madison Dunitz <madison.dunitz@chanzuckerberg.com> * rename X_approx_distribution to X_approximate_distribution (#2337) * Correctly handle non-finite numbers in heuristic determination of X distribution (#2342) * handle non-finites explicitly * improve and test edge case handling for distribution estimation * revert debugging changes * code readability * clean up type inferencing (#2332) * unit tests for 64 bit conversion * clean up type handling * type inference tests * more type inference fixes * use schema to determine user intent for data typing * stop using deprecated API * fbs type encoding test * add missing test * add more tests * correctly infer X type for CXG adaptor * lint * fix typo * ts migration * cleanup from PR review * lint * PR review changes * remove unused packages from client (#2359) * remove unused packages from client * add missing peer dep * fix: disable FE auth testing on compatibility tests (#2377) * update: release process (#2277) Co-authored-by: maniarathi <mani.arathi@gmail.com> * fix: remove spaces in param setup (#2380) * delete deploy workflow (#2396) * undo reformatting which now does not pass lint * fix snapshots which changed due to npm dep changes * add missing quoting to snapshot * another snapshot typo fix * TS Revert (2) - replay PR #2347 and #2354 (#2403) * replay edits from PR 2347 * TS Revert (3) - replay edits in PR #2327 (#2404) * replay edits in PR 2327 * TS Revert (4) - replay PR #2355 (#2405) * replay edits in PR 2355 * add additional babel config * reformat with new prettier config Co-authored-by: Severiano Badajoz <sbadajoz@chanzuckerberg.com> Co-authored-by: maniarathi <mani.arathi@gmail.com> Co-authored-by: Madison Dunitz <madison.dunitz@chanzuckerberg.com>
This commit is contained in:
Bruce Martin
co-authored by
maniarathi
Madison Dunitz
Severiano Badajoz
maniarathi
Madison Dunitz
Severiano Badajoz
parent
295590a7c6
commit
eaae6df5e3
@@ -0,0 +1,176 @@
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/* eslint-disable max-classes-per-file -- Classes are interrelated*/
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/*
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Views on the annomatrix. all API here is defined in viewCreators.js and annoMatrix.js.
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*/
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import clip from "../util/clip";
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import AnnoMatrix from "./annoMatrix";
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import { _whereCacheCreate } from "./whereCache";
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import { _isContinuousType, _getColumnSchema } from "./schema";
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class AnnoMatrixView extends AnnoMatrix {
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constructor(viewOf, rowIndex = null) {
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const nObs = rowIndex ? rowIndex.size() : viewOf.nObs;
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super(viewOf.schema, nObs, viewOf.nVar, rowIndex || viewOf.rowIndex);
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this.viewOf = viewOf;
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this.isView = true;
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}
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addObsAnnoCategory(col, category) {
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const newAnnoMatrix = this._clone();
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newAnnoMatrix.viewOf = this.viewOf.addObsAnnoCategory(col, category);
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newAnnoMatrix.schema = newAnnoMatrix.viewOf.schema;
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return newAnnoMatrix;
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}
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async removeObsAnnoCategory(col, category, unassignedCategory) {
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const newAnnoMatrix = this._clone();
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newAnnoMatrix.viewOf = await this.viewOf.removeObsAnnoCategory(
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col,
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category,
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unassignedCategory
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);
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newAnnoMatrix.schema = newAnnoMatrix.viewOf.schema;
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return newAnnoMatrix;
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}
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dropObsColumn(col) {
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const newAnnoMatrix = this._clone();
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newAnnoMatrix.viewOf = this.viewOf.dropObsColumn(col);
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newAnnoMatrix._cache.obs = this._cache.obs.dropCol(col);
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newAnnoMatrix.schema = newAnnoMatrix.viewOf.schema;
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return newAnnoMatrix;
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}
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addObsColumn(colSchema, Ctor, value) {
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const newAnnoMatrix = this._clone();
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newAnnoMatrix.viewOf = this.viewOf.addObsColumn(colSchema, Ctor, value);
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newAnnoMatrix.schema = newAnnoMatrix.viewOf.schema;
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return newAnnoMatrix;
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}
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renameObsColumn(oldCol, newCol) {
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const newAnnoMatrix = this._clone();
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newAnnoMatrix.viewOf = this.viewOf.renameObsColumn(oldCol, newCol);
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newAnnoMatrix.schema = newAnnoMatrix.viewOf.schema;
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return newAnnoMatrix;
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}
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async setObsColumnValues(col, rowLabels, value) {
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const newAnnoMatrix = this._clone();
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newAnnoMatrix.viewOf = await this.viewOf.setObsColumnValues(
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col,
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rowLabels,
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value
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);
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newAnnoMatrix._cache.obs = this._cache.obs.dropCol(col);
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newAnnoMatrix.schema = newAnnoMatrix.viewOf.schema;
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return newAnnoMatrix;
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}
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async resetObsColumnValues(col, oldValue, newValue) {
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const newAnnoMatrix = this._clone();
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newAnnoMatrix.viewOf = await this.viewOf.resetObsColumnValues(
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col,
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oldValue,
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newValue
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);
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newAnnoMatrix._cache.obs = this._cache.obs.dropCol(col);
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newAnnoMatrix.schema = newAnnoMatrix.viewOf.schema;
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return newAnnoMatrix;
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}
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addEmbedding(colSchema) {
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const newAnnoMatrix = this._clone();
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newAnnoMatrix.viewOf = this.viewOf.addEmbedding(colSchema);
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newAnnoMatrix.schema = newAnnoMatrix.viewOf.schema;
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return newAnnoMatrix;
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}
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}
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class AnnoMatrixMapView extends AnnoMatrixView {
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/*
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A view which knows how to transform its data.
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*/
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constructor(viewOf, mapFn) {
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super(viewOf);
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this.mapFn = mapFn;
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}
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async _doLoad(field, query) {
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const df = await this.viewOf._fetch(field, query);
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const dfMapped = df.mapColumns((colData, colIdx) => {
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const colLabel = df.colIndex.getLabel(colIdx);
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const colSchema = _getColumnSchema(this.schema, field, colLabel);
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return this.mapFn(field, colLabel, colSchema, colData, df);
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});
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const whereCacheUpdate = _whereCacheCreate(
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field,
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query,
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dfMapped.colIndex.labels()
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);
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return [whereCacheUpdate, dfMapped];
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}
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}
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export class AnnoMatrixClipView extends AnnoMatrixMapView {
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/*
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A view which is a clipped transformation of its parent
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*/
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constructor(viewOf, qmin, qmax) {
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super(viewOf, (field, colLabel, colSchema, colData, df) =>
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_clipAnnoMatrix(field, colLabel, colSchema, colData, df, qmin, qmax)
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);
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this.isClipped = true;
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this.clipRange = [qmin, qmax];
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Object.seal(this);
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}
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}
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export class AnnoMatrixRowSubsetView extends AnnoMatrixView {
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/*
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A view which is a subset of total rows.
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*/
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constructor(viewOf, rowIndex) {
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super(viewOf, rowIndex);
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Object.seal(this);
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}
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async _doLoad(field, query) {
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const df = await this.viewOf._fetch(field, query);
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// don't try to row-subset the var dimension.
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if (field === "var") {
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return [null, df];
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}
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const dfSubset = df.subset(null, null, this.rowIndex);
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const whereCacheUpdate = _whereCacheCreate(
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field,
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query,
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dfSubset.colIndex.labels()
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);
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return [whereCacheUpdate, dfSubset];
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}
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}
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/*
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Utility functions below
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*/
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function _clipAnnoMatrix(field, colLabel, colSchema, colData, df, qmin, qmax) {
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/* only clip obs and var scalar columns */
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if (field !== "obs" && field !== "X") return colData;
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if (!_isContinuousType(colSchema)) return colData;
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if (qmin < 0) qmin = 0;
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if (qmax > 1) qmax = 1;
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if (qmin === 0 && qmax === 1) return colData;
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const quantiles = df.col(colLabel).summarize().percentiles;
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const lower = quantiles[100 * qmin];
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const upper = quantiles[100 * qmax];
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const clippedData = clip(colData.slice(), lower, upper, Number.NaN);
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return clippedData;
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}
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/* eslint-enable max-classes-per-file -- enable*/
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