cellxgene/client/__tests__/util/stateManager/universe.test.js

/* eslint no-bitwise: "off" */

import _ from "lodash";
import * as Universe from "../../../src/util/stateManager/universe";

/*
test data mocking REST 0.2 API responses
*/
const nObs = 10;
const nVar = 32;
const field4Categories = [83, true, "foo", 2.222222];
const fieldDCategories = [99, false, "mumble", 3.1415];

const aConfigResponse = {
  config: {
    features: [
      { method: "POST", path: "/cluster/", available: false },
      { method: "POST", path: "/layout/", available: false },
      { method: "POST", path: "/diffexp/", available: false },
      { method: "POST", path: "/saveLocal/", available: false }
    ],
    displayNames: {
      engine: "the little engine that could",
      dataset: "all your zeros are mine"
    }
  }
};

const aSchemaResponse = {
  schema: {
    dataframe: {
      nObs,
      nVar,
      type: "float32"
    },
    annotations: {
      obs: [
        { name: "name", type: "string" },
        { name: "field1", type: "int32" },
        { name: "field2", type: "float32" },
        { name: "field3", type: "boolean" },
        {
          name: "field4",
          type: "categorical",
          categories: field4Categories
        }
      ],
      var: [
        { name: "name", type: "string" },
        { name: "fieldA", type: "int32" },
        { name: "fieldB", type: "float32" },
        { name: "fieldC", type: "boolean" },
        {
          name: "fieldD",
          type: "categorical",
          categories: fieldDCategories
        }
      ]
    }
  }
};

const anAnnotationsObsResponse = {
  names: ["name", "field1", "field2", "field3", "field4"],
  data: _()
    .range(nObs)
    .map(idx => [
      idx,
      `obs${idx}`,
      2 * idx,
      idx + 0.0133,
      idx & 1,
      field4Categories[idx % field4Categories.length]
    ])
    .value()
};

const anAnnotationsVarResponse = {
  names: ["fieldA", "fieldB", "fieldC", "fieldD", "name"],
  data: _()
    .range(nVar)
    .map(idx => [
      idx,
      10 * idx,
      idx + 2.90143,
      idx & 1,
      fieldDCategories[idx % fieldDCategories.length],
      `var${idx}`
    ])
    .value()
};

const aLayoutResponse = {
  layout: {
    ndims: 2,
    coordinates: _()
      .range(nObs)
      .map(idx => [idx, Math.random(), Math.random()])
      .value()
  }
};

const aDataObsResponse = {
  var: [2, 4, 29],
  obs: _()
    .range(nObs)
    .map(idx => [idx, Math.random(), Math.random(), Math.random()])
    .value()
};

describe("createUniverseFromRestV02Response", () => {
  /*
  test createUniverseFromRestV02Response - this function converts
  a set of REST 0.2 responses into a "new" Universe.

  createUniverseFromRestV02Response(
    configResponse,
    schemaResponse,
    annotationsObsResponse,
    annotationsVarResponse,
    layoutObsResponse
  ) --> Universe

  where:
  configResponse: GET /.../config
  schemaResponse: GET /.../schema
  annotationsObsResponse: GET /.../annotations/obs
  annotationsVarResponse: GET /.../annotations/var
  layoutObsResponse: GET /.../layout/obs

  See spec in docs/REST_API.md.
  */

  test("create from test data", () => {
    /*
    create a universe from sample data nad validate its shape & contents
    */

    const universe = Universe.createUniverseFromRestV02Response(
      aConfigResponse,
      aSchemaResponse,
      anAnnotationsObsResponse,
      anAnnotationsVarResponse,
      aLayoutResponse
    );

    expect(universe).toBeDefined();
    expect(universe).toMatchObject(
      expect.objectContaining({
        api: "0.2",
        nObs,
        nVar,
        schema: aSchemaResponse.schema,
        obsAnnotations: expect.any(Array),
        varAnnotations: expect.any(Array),
        obsNameToIndexMap: expect.any(Object),
        varNameToIndexMap: expect.any(Object),
        obsLayout: expect.objectContaining({
          X: expect.any(Float32Array),
          Y: expect.any(Float32Array)
        }),
        varDataCache: expect.any(Object)
      })
    );

    expect(_.size(universe.obsAnnotations)).toBe(nObs);
    expect(_.size(universe.obsNameToIndexMap)).toBe(nObs);
    expect(_.size(universe.obsLayout.X)).toBe(nObs);
    expect(_.size(universe.obsLayout.Y)).toBe(nObs);
    expect(_.size(universe.varAnnotations)).toBe(nVar);
    expect(_.size(universe.varNameToIndexMap)).toBe(nVar);
  });
});

describe("convertExpressionRESTv02ToObject", () => {
  /*
  test convertExpressionRESTv02ToObject

  convertExpressionRESTv02ToObject(
    universe,
    response) --> { geneName: Float32Array, geneName: Float32Array, ... }

  reponse is a /data/obs response:
  {
    var: [ varIndices fetched ],
    obs: [
      [ obsIndex, evalue, ... ],
      ...
    ]
  }
  */
  test("create from response data", () => {
    const universe = Universe.createUniverseFromRestV02Response(
      aConfigResponse,
      aSchemaResponse,
      anAnnotationsObsResponse,
      anAnnotationsVarResponse,
      aLayoutResponse
    );
    const expression = Universe.convertExpressionRESTv02ToObject(
      universe,
      aDataObsResponse
    );

    /* Check that the expected keys are present */
    const expectedGeneNames = _.map(
      aDataObsResponse.var,
      v => anAnnotationsVarResponse.data[v][5]
    );
    expect(Object.keys(expression)).toEqual(
      expect.arrayContaining(expectedGeneNames)
    );

    const expectedExpressionValues = _.map(
      _.unzip(aDataObsResponse.obs),
      a => new Float32Array(a)
    );

    // console.log(aDataObsResponse);
    // console.log(expression);
    // console.log(_.unzip(aDataObsResponse.obs));

    _.forEach(aDataObsResponse.var, (varIdx, idx) => {
      const varName = universe.varAnnotations[varIdx].name;
      expect(varName).toBeDefined();
      expect(varIdx).toBe(universe.varNameToIndexMap[varName]);
      expect(expression[varName]).toEqual(expectedExpressionValues[idx + 1]);
    });
  });
});