mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-10-03 01:08:12 +08:00
Dataframe, part deux - add varData and summarize() (#608)
* initial dataframe commit * initial dataframe port of core app * rename variables for clarity * remove unused import * comment out unused code * fix array handling bug in crossfilter dimension creation * allow creation of empty dataframes * handle non-existent columns * handle non-existent columns * revise tests for new dataframe * comments for clarity * comments for clarity * generate bulk add placeholder with real gene names * fix bug in gene name adding * more dataframe unit tests * fix bug - subset from current world, not universe * put cut and pasted code into a single function * improve caching of crossfilter * remove cascading update bug from graph * more performance work * improve state handling for scatterplot * performance optimization of critical path * add column summarization * dataframe utils * add callOnceLazy * fix tests * minor updates found during review * fix misspelling * remove RESTv02 from function names * comment cleanup * cut/icut col parameter defaults to null * break up large test * improve tests and comments on dataframe at/has functions * add Dataframe withCol/dropCol * expression varData now stored in a dataframe * dead code cleanup * use dataframe.summarize() * test cases for Dataframe.col.summarize * update test cases for new dataframe summarize * improve naming * use new hasCol API * add comments * add more Dataframe.withCol tests * add ability to specify row index in cut operation * retire subsetVarData function * correctly handle expression subsetting * lint and improve comments * rename cut to subset * changes based on PR review
This commit is contained in:
Bruce Martin
@@ -1,249 +0,0 @@
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import _ from "lodash";
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import * as kvCache from "../../../src/util/stateManager/keyvalcache";
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/*
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This is PRIVATE to keyvalcache and must be kept in sync with
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any changs ot that module. Need to Know - to enable error handling test
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*/
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const cachePrivateKey = "__kvcachekey__";
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/*
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helper function - promisify setTimeout()
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*/
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function timeout(ms) {
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return new Promise(resolve => setTimeout(resolve, ms));
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}
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describe("kvcache API", () => {
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/*
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test the happy path create/set/get API
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*/
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test("simple create", () => {
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/* with defaults */
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const kvc = kvCache.create();
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expect(kvc).toBeDefined();
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expect(kvc).toEqual(expect.objectContaining({}));
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expect(kvCache.get(kvc, "test")).toBeUndefined();
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/* with params */
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const kvc1 = kvCache.create(/* lowWatermark */ 99, /* minTTL */ 0);
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expect(kvc1).toBeDefined();
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expect(kvc1).toEqual(expect.objectContaining({}));
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});
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test("set/get", () => {
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/*
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- check basic get/set functionality
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- check set does not mutate source cache
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*/
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const keyName = "foo";
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const kvc1 = kvCache.create();
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expect(kvc1).toBeDefined();
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expect(kvCache.get(kvc1, keyName)).toBeUndefined();
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const val2 = [2];
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const kvc2 = kvCache.set(kvc1, keyName, val2);
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expect(kvc2).toBeDefined();
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expect(kvc2).not.toBe(kvc1);
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expect(kvCache.get(kvc1, keyName)).toBeUndefined();
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expect(kvCache.get(kvc2, keyName)).toBe(val2);
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const val3 = [3];
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const kvc3 = kvCache.set(kvc2, keyName, val3);
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expect(kvc3).toBeDefined();
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expect(kvc3).not.toBe(kvc1);
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expect(kvc3).not.toBe(kvc2);
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expect(kvCache.get(kvc1, keyName)).toBeUndefined();
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expect(kvCache.get(kvc2, keyName)).toBe(val2);
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expect(kvCache.get(kvc3, keyName)).toBe(val3);
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});
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});
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describe("common error handling", () => {
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/*
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Test common error handlers
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*/
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test("set() protection from namespace pollution", () => {
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/*
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Test that set() will not allow use of the private cache key
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*/
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const kvc = kvCache.create();
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expect(() => {
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kvCache.set(kvc, cachePrivateKey, {});
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}).toThrow();
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});
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test("create() does not accept bogus config", () => {
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expect(() => {
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kvCache.create([], {});
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}).toThrow();
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expect(() => {
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kvCache.create(-99, 0);
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}).toThrow();
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expect(() => {
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kvCache.create(100, -1);
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}).toThrow();
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expect(() => {
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kvCache.create(1000, "foobar");
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}).toThrow();
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expect(() => {
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kvCache.create(null, 8);
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}).toThrow();
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});
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});
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describe("map", () => {
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/*
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Test kvCache.map() - create new cache that is a transformation of an
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existing cache
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*/
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test("map of empty cache", () => {
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const kvc = kvCache.create();
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const callback = jest.fn();
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const kvcMapped = kvCache.map(kvc, callback);
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expect(callback).not.toHaveBeenCalled();
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expect(kvcMapped).toBeDefined();
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expect(kvcMapped).not.toBe(kvc); // immutable operation
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expect(kvcMapped).toEqual(kvc);
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});
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test("map of non-empty cache", () => {
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const key = "aKey";
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const val = [0, 1, 2];
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let kvc = kvCache.create();
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kvc = kvCache.set(kvc, key, val);
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const mockCB = jest.fn().mockImplementation(v => [...v]);
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const kvcMapped = kvCache.map(kvc, mockCB);
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expect(kvcMapped).toBeDefined();
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expect(kvcMapped).not.toBe(kvc); // immutable operation
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expect(_.isEqual(kvc, kvcMapped)).toBe(true);
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expect(mockCB).toHaveBeenCalledTimes(1);
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expect(mockCB).toHaveBeenLastCalledWith(val, key);
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});
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});
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describe("flush", () => {
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/*
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test various cache flush behavior
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*/
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test("flush - lowWatermark, disable minTTL", () => {
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/*
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verify lowWatermark functions correctly
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*/
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// set lowWatermark to 2, set three times - only the final two
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// should remain.
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let kvc = kvCache.create(2, 0);
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["a", "b", "c"].forEach(k => {
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kvc = kvCache.set(kvc, k, []);
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});
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expect(kvc).toEqual(
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expect.objectContaining({
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b: expect.arrayContaining([]),
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c: expect.arrayContaining([])
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})
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);
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expect(kvc).toEqual(
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expect.not.objectContaining({
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a: expect.arrayContaining([])
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})
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);
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});
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test("flush - minTTL, disable lowWatermark", async () => {
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/*
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verify minTTL functions correctly
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*/
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// set minTTL to 1 ms
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let kvc = kvCache.create(0, 10);
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kvc = kvCache.set(kvc, "a", []);
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await timeout(20);
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["b", "c"].forEach(k => {
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kvc = kvCache.set(kvc, k, []);
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});
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expect(kvc).toEqual(
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expect.objectContaining({
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b: expect.arrayContaining([]),
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c: expect.arrayContaining([])
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})
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);
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expect(kvc).toEqual(
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expect.not.objectContaining({
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a: expect.arrayContaining([])
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})
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);
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});
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test("flush - minTTL and lowWatermark", async () => {
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/*
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verify minTTL functions correctly
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*/
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// set lowwatermark to 3, minTTL to 1 ms
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let kvc = kvCache.create(3, 10);
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kvc = kvCache.set(kvc, "a", []);
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// delay
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await timeout(20);
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["b", "c"].forEach(k => {
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kvc = kvCache.set(kvc, k, []);
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});
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expect(kvc).toEqual(
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expect.objectContaining({
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a: expect.arrayContaining([]),
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b: expect.arrayContaining([]),
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c: expect.arrayContaining([])
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})
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);
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kvc = kvCache.set(kvc, "d", []);
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expect(kvc).toEqual(
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expect.objectContaining({
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b: expect.arrayContaining([]),
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c: expect.arrayContaining([]),
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d: expect.arrayContaining([])
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})
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);
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expect(kvc).toEqual(
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expect.not.objectContaining({
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a: expect.arrayContaining([])
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})
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);
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});
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test("manual flush", async () => {
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let kvc = kvCache.create(1, 10);
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["a", "b", "c", "d"].forEach(k => {
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kvc = kvCache.set(kvc, k, []);
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});
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// Before TTL has expired, should have all values in cache.
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expect(kvc).toEqual(
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expect.objectContaining({
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a: expect.arrayContaining([]),
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b: expect.arrayContaining([]),
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c: expect.arrayContaining([])
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})
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);
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// let TTL expire
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await timeout(10);
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// manually flush
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const postFlushKvc = kvCache.flush(kvc);
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expect(postFlushKvc).toBeDefined();
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expect(postFlushKvc).not.toBe(kvc);
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expect(postFlushKvc).toEqual(
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expect.objectContaining({
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d: expect.arrayContaining([])
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})
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);
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});
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});
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@@ -1,291 +0,0 @@
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import summarizeAnnotations from "../../../src/util/stateManager/summarizeAnnotations";
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import * as Dataframe from "../../../src/util/dataframe";
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function float32Conversion(f) {
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return new Float32Array([39.3])[0];
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}
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describe("summarizeAnnotations", () => {
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const schema = {
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annotations: {
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obs: [
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{ name: "name", type: "string" },
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{ name: "nameString", type: "string" },
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{ name: "nameBoolean", type: "boolean" },
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{ name: "nameFloat32", type: "float32" },
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{ name: "nameInt32", type: "int32" },
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{
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name: "nameCategorical",
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type: "categorical",
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categories: [true, false, 1, 0, 0.00001, 4383.4833, "test", "", "0"]
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}
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],
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var: [{ name: "name", type: "string" }]
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}
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};
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test("empty test", () => {
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const df = Dataframe.Dataframe.empty();
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const summary = summarizeAnnotations(schema, df, df.clone());
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expect(summary).toEqual(
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expect.objectContaining({
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obs: {
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nameString: {
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categorical: true,
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categories: [],
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categoryCounts: new Map(),
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numCategories: 0
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},
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nameBoolean: {
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categorical: true,
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categories: [],
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categoryCounts: new Map(),
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numCategories: 0
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},
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nameFloat32: {
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categorical: false,
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range: {
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max: undefined,
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min: undefined,
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nan: 0,
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ninf: 0,
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pinf: 0
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}
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},
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nameInt32: {
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categorical: false,
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range: {
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max: undefined,
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min: undefined,
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nan: 0,
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ninf: 0,
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pinf: 0
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}
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},
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nameCategorical: {
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categorical: true,
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categories: [],
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categoryCounts: new Map(),
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numCategories: 0
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}
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},
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var: {}
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})
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);
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});
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test("simple test", () => {
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const obsAnnotations = new Dataframe.Dataframe(
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[1, 6],
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[
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["n1"],
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["hi"],
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[true],
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new Float32Array([39.3]),
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new Int32Array([99]),
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[1]
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],
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null,
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new Dataframe.KeyIndex([
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"name",
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"nameString",
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"nameBoolean",
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"nameFloat32",
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"nameInt32",
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"nameCategorical"
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])
|
||||
);
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const varAnnotations = Dataframe.Dataframe.empty();
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const summary = summarizeAnnotations(
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schema,
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obsAnnotations,
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varAnnotations
|
||||
);
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expect(summary).toEqual(
|
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expect.objectContaining({
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obs: {
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nameString: {
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categorical: true,
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categories: ["hi"],
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categoryCounts: new Map([["hi", 1]]),
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numCategories: 1
|
||||
},
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nameBoolean: {
|
||||
categorical: true,
|
||||
categories: [true],
|
||||
categoryCounts: new Map([[true, 1]]),
|
||||
numCategories: 1
|
||||
},
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nameFloat32: {
|
||||
categorical: false,
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||||
range: {
|
||||
min: float32Conversion(39.3),
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max: float32Conversion(39.3),
|
||||
nan: 0,
|
||||
ninf: 0,
|
||||
pinf: 0
|
||||
}
|
||||
},
|
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nameInt32: {
|
||||
categorical: false,
|
||||
range: { min: 99, max: 99, nan: 0, ninf: 0, pinf: 0 }
|
||||
},
|
||||
nameCategorical: {
|
||||
categorical: true,
|
||||
categories: [1],
|
||||
categoryCounts: new Map([[1, 1]]),
|
||||
numCategories: 1
|
||||
}
|
||||
},
|
||||
var: {}
|
||||
})
|
||||
);
|
||||
});
|
||||
|
||||
test("multi test", () => {
|
||||
const obsAnnotations = new Dataframe.Dataframe(
|
||||
[3, 6],
|
||||
[
|
||||
["n0", "n1", "n2"],
|
||||
["hi", "hi", "bye"],
|
||||
[false, true, true],
|
||||
new Float32Array([39.3, 39.3, 0]),
|
||||
new Int32Array([99, 99, 99]),
|
||||
[1, false, "0"]
|
||||
],
|
||||
null,
|
||||
new Dataframe.KeyIndex([
|
||||
"name",
|
||||
"nameString",
|
||||
"nameBoolean",
|
||||
"nameFloat32",
|
||||
"nameInt32",
|
||||
"nameCategorical"
|
||||
])
|
||||
);
|
||||
const varAnnotations = Dataframe.Dataframe.empty();
|
||||
|
||||
const summary = summarizeAnnotations(
|
||||
schema,
|
||||
obsAnnotations,
|
||||
varAnnotations
|
||||
);
|
||||
|
||||
expect(summary).toMatchObject(
|
||||
expect.objectContaining({
|
||||
obs: {
|
||||
nameString: {
|
||||
categorical: true,
|
||||
categories: expect.arrayContaining(["hi", "bye"]),
|
||||
categoryCounts: new Map([["hi", 2], ["bye", 1]]),
|
||||
numCategories: 2
|
||||
},
|
||||
nameBoolean: {
|
||||
categorical: true,
|
||||
categories: expect.arrayContaining([true, false]),
|
||||
categoryCounts: new Map([[true, 2], [false, 1]]),
|
||||
numCategories: 2
|
||||
},
|
||||
nameFloat32: {
|
||||
categorical: false,
|
||||
range: {
|
||||
min: 0,
|
||||
max: float32Conversion(39.3),
|
||||
nan: 0,
|
||||
ninf: 0,
|
||||
pinf: 0
|
||||
}
|
||||
},
|
||||
nameInt32: {
|
||||
categorical: false,
|
||||
range: { min: 99, max: 99, nan: 0, ninf: 0, pinf: 0 }
|
||||
},
|
||||
nameCategorical: {
|
||||
categorical: true,
|
||||
categories: expect.arrayContaining([1, false, "0"]),
|
||||
categoryCounts: new Map([[1, 1], [false, 1], ["0", 1]]),
|
||||
numCategories: 3
|
||||
}
|
||||
},
|
||||
var: {}
|
||||
})
|
||||
);
|
||||
});
|
||||
|
||||
test("non-finite numbers", () => {
|
||||
const obsAnnotations = new Dataframe.Dataframe(
|
||||
[4, 6],
|
||||
[
|
||||
["n0", "n1", "n2", "n2"],
|
||||
["hi", "hi", "bye", "bye"],
|
||||
[false, true, true, true],
|
||||
new Float32Array([
|
||||
39.3,
|
||||
Number.NEGATIVE_INFINITY,
|
||||
Number.NaN,
|
||||
Number.POSITIVE_INFINITY
|
||||
]),
|
||||
new Int32Array([99, 99, 99, 99]),
|
||||
[1, false, "0", "0"]
|
||||
],
|
||||
null,
|
||||
new Dataframe.KeyIndex([
|
||||
"name",
|
||||
"nameString",
|
||||
"nameBoolean",
|
||||
"nameFloat32",
|
||||
"nameInt32",
|
||||
"nameCategorical"
|
||||
])
|
||||
);
|
||||
const varAnnotations = Dataframe.Dataframe.empty();
|
||||
|
||||
const summary = summarizeAnnotations(
|
||||
schema,
|
||||
obsAnnotations,
|
||||
varAnnotations
|
||||
);
|
||||
|
||||
expect(summary).toMatchObject(
|
||||
expect.objectContaining({
|
||||
obs: {
|
||||
nameString: {
|
||||
categorical: true,
|
||||
categories: expect.arrayContaining(["hi", "bye"]),
|
||||
categoryCounts: new Map([["hi", 2], ["bye", 1]]),
|
||||
numCategories: 2
|
||||
},
|
||||
nameBoolean: {
|
||||
categorical: true,
|
||||
categories: expect.arrayContaining([true, false]),
|
||||
categoryCounts: new Map([[true, 2], [false, 1]]),
|
||||
numCategories: 2
|
||||
},
|
||||
nameFloat32: {
|
||||
categorical: false,
|
||||
range: {
|
||||
min: float32Conversion(39.3),
|
||||
max: float32Conversion(39.3),
|
||||
nan: 1,
|
||||
ninf: 1,
|
||||
pinf: 1
|
||||
}
|
||||
},
|
||||
nameInt32: {
|
||||
categorical: false,
|
||||
range: { min: 99, max: 99, nan: 0, ninf: 0, pinf: 0 }
|
||||
},
|
||||
nameCategorical: {
|
||||
categorical: true,
|
||||
categories: expect.arrayContaining([1, false, "0"]),
|
||||
categoryCounts: new Map([[1, 1], [false, 1], ["0", 1]]),
|
||||
numCategories: 3
|
||||
}
|
||||
},
|
||||
var: {}
|
||||
})
|
||||
);
|
||||
});
|
||||
});
|
||||
@@ -41,15 +41,13 @@ describe("createUniverseFromResponse", () => {
|
||||
expect(universe).toBeDefined();
|
||||
expect(universe).toMatchObject(
|
||||
expect.objectContaining({
|
||||
api: "0.2",
|
||||
nObs,
|
||||
nVar,
|
||||
schema: REST.schema.schema,
|
||||
obsAnnotations: expect.any(Dataframe.Dataframe),
|
||||
varAnnotations: expect.any(Dataframe.Dataframe),
|
||||
obsLayout: expect.any(Dataframe.Dataframe),
|
||||
summary: expect.any(Object),
|
||||
varDataCache: expect.any(Object)
|
||||
varData: expect.any(Dataframe.Dataframe)
|
||||
})
|
||||
);
|
||||
|
||||
@@ -63,5 +61,6 @@ describe("createUniverseFromResponse", () => {
|
||||
nVar,
|
||||
REST.schema.schema.annotations.var.length
|
||||
]);
|
||||
expect(universe.varData.isEmpty()).toBeTruthy();
|
||||
});
|
||||
});
|
||||
|
||||
@@ -8,7 +8,6 @@ import {
|
||||
obsAnnoDimensionName,
|
||||
layoutDimensionName
|
||||
} from "../../../src/util/nameCreators";
|
||||
import * as kvCache from "../../../src/util/stateManager/keyvalcache";
|
||||
|
||||
/*
|
||||
Helper - creates universe, world, corssfilter and dimensionMap from
|
||||
@@ -55,28 +54,13 @@ describe("createWorldFromEntireUniverse", () => {
|
||||
|
||||
expect(world).toMatchObject(
|
||||
expect.objectContaining({
|
||||
api: "0.2",
|
||||
nObs: universe.nObs,
|
||||
nVar: universe.nVar,
|
||||
schema: universe.schema,
|
||||
obsAnnotations: universe.obsAnnotations,
|
||||
varAnnotations: universe.varAnnotations,
|
||||
obsLayout: universe.obsLayout,
|
||||
|
||||
summary: expect.objectContaining({
|
||||
obs: _(REST.schema.schema.annotations.obs)
|
||||
.filter(v => v.name !== "name")
|
||||
.keyBy("name")
|
||||
.mapValues(() => expect.any(Object))
|
||||
.value(),
|
||||
var: _(REST.schema.schema.annotations.var)
|
||||
.filter(v => v.name !== "name")
|
||||
.keyBy("name")
|
||||
.mapValues(() => expect.any(Object))
|
||||
.value()
|
||||
}),
|
||||
|
||||
varDataCache: expect.any(Object)
|
||||
varData: expect.any(Dataframe.Dataframe)
|
||||
})
|
||||
);
|
||||
});
|
||||
@@ -121,18 +105,13 @@ describe("createWorldFromCurrentSelection", () => {
|
||||
|
||||
expect(world).toMatchObject(
|
||||
expect.objectContaining({
|
||||
api: "0.2",
|
||||
nObs: matchingIndices.length,
|
||||
nVar: universe.nVar,
|
||||
schema: universe.schema,
|
||||
obsAnnotations: expect.any(Dataframe.Dataframe),
|
||||
varAnnotations: universe.varAnnotations,
|
||||
obsLayout: expect.any(Dataframe.Dataframe),
|
||||
summary: {
|
||||
obs: expect.any(Object) /* we could do better! */,
|
||||
var: expect.any(Object) /* we could do better! */
|
||||
},
|
||||
varDataCache: expect.any(Object)
|
||||
varData: expect.any(Dataframe.Dataframe)
|
||||
})
|
||||
);
|
||||
|
||||
@@ -183,60 +162,14 @@ describe("createObsDimensionMap", () => {
|
||||
});
|
||||
});
|
||||
|
||||
describe("subsetVarData", () => {
|
||||
test("when world eq universe", () => {
|
||||
const { universe, world } = defaultBigBang();
|
||||
/* create a mock varData array for subsetting */
|
||||
const sourceVarData = new Float32Array(universe.nObs);
|
||||
|
||||
/* expect literally the same object back */
|
||||
const result = World.subsetVarData(world, universe, sourceVarData);
|
||||
expect(result).toBe(sourceVarData);
|
||||
});
|
||||
|
||||
test("when world neq universe", () => {
|
||||
const { universe, world, crossfilter, dimensionMap } = defaultBigBang();
|
||||
/* create a mock varData array for subsetting */
|
||||
const sourceVarData = Float32Array.from(_.range(universe.nObs));
|
||||
|
||||
/* mock a selection */
|
||||
dimensionMap[obsAnnoDimensionName("field1")].filterRange([0, 5]);
|
||||
dimensionMap[obsAnnoDimensionName("field3")].filterExact(false);
|
||||
|
||||
/* create the world from the selection */
|
||||
const newWorld = World.createWorldFromCurrentSelection(
|
||||
universe,
|
||||
world,
|
||||
crossfilter
|
||||
);
|
||||
expect(newWorld.obsAnnotations.rowIndex.keys()).toEqual(
|
||||
new Int32Array([0, 2])
|
||||
);
|
||||
|
||||
/* expect a subset */
|
||||
const result = World.subsetVarData(newWorld, universe, sourceVarData);
|
||||
expect(result).not.toBe(sourceVarData);
|
||||
expect(result).toHaveLength(newWorld.nObs);
|
||||
/* check that we have expected source var content */
|
||||
expect(result).toMatchObject(new Float32Array([0, 2]));
|
||||
});
|
||||
});
|
||||
|
||||
describe("createVarDimension", () => {
|
||||
describe("createVarDataDimension", () => {
|
||||
/* create default universe */
|
||||
const { world, crossfilter } = defaultBigBang();
|
||||
/* create a mock var data cache */
|
||||
const varDataCache = kvCache.set(
|
||||
kvCache.create(),
|
||||
world.varData = world.varData.withCol(
|
||||
"GENE",
|
||||
Float32Array.from(_.range(world.nObs))
|
||||
);
|
||||
const result = World.createVarDimension(
|
||||
world,
|
||||
varDataCache,
|
||||
crossfilter,
|
||||
"GENE"
|
||||
);
|
||||
const result = World.createVarDataDimension(world, crossfilter, "GENE");
|
||||
expect(result).toBeInstanceOf(Crossfilter.ScalarDimension);
|
||||
});
|
||||
|
||||
|
||||
Reference in New Issue
Block a user