cellxgene/client/__tests__/e2e/e2e.test.js

/*
Smoke test suite that will be run in Travis CI

Tests included in this file are expected to be relatively stable and test core features
 */
import { appUrlBase, DATASET } from "./config";
import { setupTestBrowser } from "./testBrowser";
import { datasets } from "./data";

let browser, page, utils, cxgActions;
const data = datasets[DATASET];

beforeAll(async () => {
  const browserViewport = { width: 1280, height: 960 };
  [browser, page, utils, cxgActions] = await setupTestBrowser(browserViewport);
});

beforeEach(async () => {
  await page.goto(appUrlBase);
});

afterAll(() => {
  if (browser !== undefined) browser.close();
});

describe("did launch", () => {
  test("page launched", async () => {
    const element = await utils.getOneElementInnerHTML("[data-testid='header']");
    expect(element).toBe(data.title);
  });
});

describe("metadata loads", () => {
  test("categories and values from dataset appear", async () => {
    for (const label in data.categorical) {
      await utils.waitByID(`category-${label}`);
      const categoryName = await utils.getOneElementInnerText(`[data-testid="category-${label}"]`);
      expect(categoryName).toMatch(label);
      await utils.clickOn(`${label}:category-expand`);
      const categories = await cxgActions.getAllCategoriesAndCounts(label);
      expect(Object.keys(categories)).toMatchObject(
        Object.keys(data.categorical[label])
      );
      expect(Object.values(categories)).toMatchObject(
        Object.values(data.categorical[label])
      );
    }
  });

  test("continuous data appears", async () => {
    for (const label in data.continuous) {
      await utils.waitByID(`histogram-${label}`);
    }
  });
});

describe("cell selection", () => {
  test("selects all cells cellset 1", async () => {
    const cellCount = await cxgActions.cellSet(1);
    expect(cellCount).toBe(data.dataframe.nObs);
  });

  test("selects all cells cellset 2", async () => {
    const cellCount = await cxgActions.cellSet(2);
    expect(cellCount).toBe(data.dataframe.nObs);
  });

  test("selects cells via lasso", async () => {
    for (const cellset of data.cellsets.lasso) {
      const cellset1 = await cxgActions.calcDragCoordinates(
        "layout-graph",
        cellset["coordinates-as-percent"]
      );
      await cxgActions.drag("layout-graph", cellset1.start, cellset1.end, true);
      const cellCount = await cxgActions.cellSet(1);
      expect(cellCount).toBe(cellset.count);
    }
  });

  test("selects cells via categorical", async () => {
    for (const cellset of data.cellsets.categorical) {
      await utils.clickOn(`${cellset.metadata}:category-expand`);
      await utils.clickOn(`${cellset.metadata}:category-select`);
      for (const val of cellset.values) {
        await utils.clickOn(`categorical-value-select-${cellset.metadata}-${val}`);
      }
      const cellCount = await cxgActions.cellSet(1);
      expect(cellCount).toBe(cellset.count);
    }
  });

  test("selects cells via continuous", async () => {
    for (const cellset of data.cellsets.continuous) {
      const histBrushableAreaId = `histogram-${cellset.metadata}-plot-brushable-area`;
      const coords = await cxgActions.calcDragCoordinates(
        histBrushableAreaId,
        cellset["coordinates-as-percent"]
      );
      await cxgActions.drag(histBrushableAreaId, coords.start, coords.end);
      const cellCount = await cxgActions.cellSet(1);
      expect(cellCount).toBe(cellset.count);
    }
  });
});

describe("gene entry", () => {
  test("search for single gene", async () => cxgActions.addGeneToSearch(data.genes.search));

  test("bulk add genes", async () => {
    const testGenes = data.genes.bulkadd;
    await cxgActions.bulkAddGenes(testGenes);
    const allHistograms = await cxgActions.getAllHistograms("histogram-user-gene", testGenes);
    expect(allHistograms).toEqual(expect.arrayContaining(testGenes));
    expect(allHistograms.length).toEqual(testGenes.length);
  });
});

describe("differential expression", () => {
  test("selects cells, saves them and performs diffexp", async () => {
    await cxgActions.runDiffExp(data.diffexp.cellset1, data.diffexp.cellset2);
    const allHistograms = await cxgActions.getAllHistograms(
      "histogram-diffexp",
      data.diffexp["gene-results"]
    );
    expect(allHistograms).toEqual(
      expect.arrayContaining(data.diffexp["gene-results"])
    );
    expect(allHistograms.length).toEqual(data.diffexp["gene-results"].length);
  });
});

describe("subset", () => {
  test("subset - cell count matches", async () => {
    for (const select of data.subset.cellset1) {
      if (select.kind === "categorical") {
        await cxgActions.selectCategory(select.metadata, select.values, true);
      }
    }
    await utils.clickOn("subset-button");
    for (const label in data.subset.categorical) {
      const categories = await cxgActions.getAllCategoriesAndCounts(label);
      expect(Object.keys(categories)).toMatchObject(
        Object.keys(data.subset.categorical[label])
      );
      expect(Object.values(categories)).toMatchObject(
        Object.values(data.subset.categorical[label])
      );
    }
  });

  test("lasso after subset", async () => {
    for (const select of data.subset.cellset1) {
      if (select.kind === "categorical") {
        await cxgActions.selectCategory(select.metadata, select.values, true);
      }
    }
    await utils.clickOn("subset-button");
    const lassoSelection = await cxgActions.calcDragCoordinates(
      "layout-graph",
      data.subset.lasso["coordinates-as-percent"]
    );
    await cxgActions.drag(
      "layout-graph",
      lassoSelection.start,
      lassoSelection.end,
      true
    );
    const cellCount = await cxgActions.cellSet(1);
    expect(cellCount).toBe(data.subset.lasso.count);
  });

  test("undo selection appends the top diff exp genes to user defined genes", async () => {
    const userDefinedGenes = data.genes.bulkadd;
    const diffExpGenes = data.diffexp["gene-results"];
    await cxgActions.bulkAddGenes(userDefinedGenes);
    const userDefinedHistograms = await cxgActions.getAllHistograms("histogram-user-gene", userDefinedGenes);
    expect(userDefinedHistograms).toEqual(expect.arrayContaining(userDefinedGenes));
    await cxgActions.subset({x1: 0.15, y1: 0.10, x2: 0.98, y2: 0.98});
    await cxgActions.runDiffExp(data.diffexp.cellset1, data.diffexp.cellset2);
    const diffExpHistograms = await cxgActions.getAllHistograms("histogram-diffexp", diffExpGenes);
    expect(diffExpHistograms).toEqual(expect.arrayContaining(diffExpGenes));
    await utils.clickOn("reset-subset-button");
    const expected = [].concat(userDefinedGenes, diffExpGenes);
    const userDefinedHistogramsAfterSubset = await cxgActions.getAllHistograms(
      "histogram-user-gene",
      expected
    );
    expect(userDefinedHistogramsAfterSubset).toEqual(expect.arrayContaining(expected));
  });

  test("subset selection appends the top diff exp genes to user defined genes", async () => {
    const userDefinedGenes = data.genes.bulkadd;
    const diffExpGenes = data.diffexp["gene-results"];
    await cxgActions.bulkAddGenes(userDefinedGenes);
    const userDefinedHistograms = await cxgActions.getAllHistograms("histogram-user-gene", userDefinedGenes);
    expect(userDefinedHistograms).toEqual(expect.arrayContaining(userDefinedGenes));
    await cxgActions.subset({x1: 0.15, y1: 0.10, x2: 0.98, y2: 0.98});
    await cxgActions.runDiffExp(data.diffexp.cellset1, data.diffexp.cellset2);
    const diffExpHistograms = await cxgActions.getAllHistograms("histogram-diffexp", diffExpGenes);
    expect(diffExpHistograms).toEqual(expect.arrayContaining(diffExpGenes));
    await cxgActions.subset({x1: 0.16, y1: 0.11, x2: 0.97, y2: 0.97});
    const expected = [].concat(userDefinedGenes, diffExpGenes);
    const userDefinedHistogramsAfterSubset = await cxgActions.getAllHistograms(
      "histogram-user-gene",
      expected
    );
    expect(userDefinedHistogramsAfterSubset).toEqual(expect.arrayContaining(expected));
  });
});

describe("scatter plot", () => {
  test("scatter plot appears", async () => {
    await cxgActions.bulkAddGenes(Object.values(data.scatter.genes));
    await utils.clickOn(`plot-x-${data.scatter.genes.x}`);
    await utils.clickOn(`plot-y-${data.scatter.genes.y}`);
    await utils.waitByID("scatterplot");
  });
});

describe("clipping", () => {
  test("clip continuous", async () => {
    await cxgActions.clip(data.clip.min, data.clip.max);
    const histBrushableAreaId = `histogram-${data.clip.metadata}-plot-brushable-area`;
    const coords = await cxgActions.calcDragCoordinates(
      histBrushableAreaId,
      data.clip["coordinates-as-percent"]
    );
    await cxgActions.drag(histBrushableAreaId, coords.start, coords.end);
    const cellCount = await cxgActions.cellSet(1);
    expect(cellCount).toBe(data.clip.count);
  });

  test("clip gene", async () => {
    await utils.typeInto("gene-search", data.clip.gene);
    await page.keyboard.press("Enter");
    await page.waitForSelector(`[data-testid='histogram-${data.clip.gene}']`);
    await cxgActions.clip(data.clip.min, data.clip.max);
    const histBrushableAreaId = `histogram-${data.clip.gene}-plot-brushable-area`;
    const coords = await cxgActions.calcDragCoordinates(
      histBrushableAreaId,
      data.clip["coordinates-as-percent"]
    );
    await cxgActions.drag(histBrushableAreaId, coords.start, coords.end);
    const cellCount = await cxgActions.cellSet(1);
    expect(cellCount).toBe(data.clip["gene-cell-count"]);
  });
});

// interact with UI elements just that they do not break
describe("ui elements don't error", () => {
  test("color by", async () => {
    for (const label in data.categorical) {
      await utils.clickOn(`colorby-${label}`);
    }
    for (const label in data.continuous) {
      await utils.clickOn(`colorby-${label}`);
    }
  });

  test("color by for gene", async () => {
    await utils.typeInto("gene-search", data.genes.search);
    await page.keyboard.press("Enter");
    await page.waitForSelector(
      `[data-testid='histogram-${data.genes.search}']`
    );
    await utils.clickOn(`colorby-${data.genes.search}`);
  });

  test("pan and zoom", async () => {
    await utils.clickOn("mode-pan-zoom");
    const panCoords = await cxgActions.calcDragCoordinates(
      "layout-graph",
      data.pan["coordinates-as-percent"]
    );
    await cxgActions.drag(
      "layout-graph",
      panCoords.start,
      panCoords.end,
      false
    );
    await page.evaluate("window.scrollBy(0, 1000);");
  });
});

describe("centroid labels", () => {
  test("labels are created", async () => {
    await utils.clickOn("centroid-label-toggle");
    const labels = Object.keys(data.categorical);
    /* eslint-disable no-await-in-loop */
    // Toggle colorby for each category and check to see if labels are generated
    for (let i = 0, { length } = labels; i < length; i += 1) {
      const label = labels[i];
      await utils.clickOn(`colorby-${label}`);
      const generatedLabels = await utils.getAllByClass("centroid-label");
      // Number of labels generated should be equal to size of the object
      expect(generatedLabels).toHaveLength(
        Object.keys(data.categorical[label]).length
      );
    }
    /* eslint-enable no-await-in-loop */
  });
});

describe("graph overlay", () => {
  test("transform centroids correctly", async () => {
    const category = Object.keys(data.categorical)[0];
    await utils.clickOn("centroid-label-toggle");
    await utils.clickOn(`colorby-${category}`);
    await utils.clickOn("mode-pan-zoom");
    const panCoords = await cxgActions.calcDragCoordinates(
      "layout-graph",
      data.pan["coordinates-as-percent"]
    );

    const categoryValue = Object.keys(data.categorical[category])[0];
    const initialCoordinates = await utils.getElementCoordinates(
      `${categoryValue}-centroid-label`
    );
    await cxgActions.drag(
      "layout-graph",
      panCoords.start,
      panCoords.end,
      false
    );
    const terminalCoordinates = await utils.getElementCoordinates(
      `${categoryValue}-centroid-label`
    );
    expect(terminalCoordinates[0] - initialCoordinates[0]).toBeCloseTo(
      panCoords.end.x - panCoords.start.x
    );
    expect(terminalCoordinates[1] - initialCoordinates[1]).toBeCloseTo(
      panCoords.end.y - panCoords.start.y
    );
  });
});