genesets e2e tests (#2241)

* __test: create geneset * example dataset test geneset * delete geneset test * edit __test * gene crud * Update client/Makefile Co-authored-by: Severiano Badajoz <sbadajoz@chanzuckerberg.com> * copy gene sets separately * make fix * ignore test files locally * csv update * updated csvs * fix unit tests for gene set load routes * add missing fix to czi_hosted unit test * pin tiledb version, for czi_hosted backend, to <0.9 * Revert tiledb pin to be less than 0.9. Broken tests have been updated in main branch. * newline, gitignore * color by and subset * diffexp sets equal * add diff exp test class * fix data class * diffexp snapshot * snapshot * snap3 * snapshot parentInnerhtml * remove snap * updated anno snaps * add test class to gene list div * new snapshots * kick off * Revert "kick off" This reverts commit 743f551d55. * remove import * eol * revert changes to csv re: gene tests * global name Co-authored-by: Severiano Badajoz <sbadajoz@chanzuckerberg.com> Co-authored-by: bkmartinjr <bruce@chanzuckerberg.com> Co-authored-by: Arathi Mani <arathi.mani@chanzuckerberg.com> Co-authored-by: maniarathi <mani.arathi@gmail.com>
2026-10-03 00:48:12 +08:00 · 2021-07-01 21:29:06 -04:00
parent b714c18e75
commit face1b3033
21 changed files with 564 additions and 47 deletions
@@ -176,6 +176,137 @@ export async function createCategory(categoryName) {
  await clickOn("submit-category");
 }

+/* 
+
+  GENESET 
+
+*/
+
+export async function colorByGeneset(genesetName) {
+  await clickOn(`${genesetName}:colorby-entire-geneset`);
+}
+
+export async function colorByGene(gene) {
+  await clickOn(`colorby-${gene}`);
+}
+
+export async function assertColorLegendLabel(label) {
+  const handle = await waitByID("continuous_legend_color_by_label");
+
+  const result = await handle.evaluate((node) => {
+    return node.getAttribute("aria-label");
+  });
+
+  return expect(result).toBe(label);
+}
+
+export async function expandGeneset(genesetName) {
+  const expand = await waitByID(`${genesetName}:geneset-expand`);
+  const notExpanded = await expand.$(
+    "[data-testclass='geneset-expand-is-not-expanded']"
+  );
+  if (notExpanded) await clickOn(`${genesetName}:geneset-expand`);
+}
+
+export async function createGeneset(genesetName) {
+  await clickOnUntil("open-create-geneset-dialog", async () => {
+    await expect(page).toMatchElement(getTestId("create-geneset-input"));
+  });
+
+  await typeInto("create-geneset-input", genesetName);
+  await clickOn("submit-geneset");
+  await waitByClass("autosave-complete");
+}
+
+export async function editGenesetName(genesetName, editText) {
+  const editButton = `${genesetName}:edit-genesetName-mode`;
+  const submitButton = `${genesetName}:submit-geneset`;
+  await clickOnUntil(`${genesetName}:see-actions`, async () => {
+    await expect(page).toMatchElement(getTestId(editButton));
+  });
+  await clickOn(editButton);
+  await typeInto("rename-geneset-modal", editText);
+  await clickOn(submitButton);
+}
+
+export async function deleteGeneset(genesetName) {
+  const targetId = `${genesetName}:delete-geneset`;
+
+  await clickOnUntil(`${genesetName}:see-actions`, async () => {
+    await expect(page).toMatchElement(getTestId(targetId));
+  });
+
+  await clickOn(targetId);
+
+  await assertGenesetDoesNotExist(genesetName);
+  await waitByClass("autosave-complete");
+}
+
+export async function assertGenesetDoesNotExist(genesetName) {
+  const result = await isElementPresent(
+    getTestId(`${genesetName}:geneset-name`)
+  );
+  await expect(result).toBe(false);
+}
+
+export async function assertGenesetExists(genesetName) {
+  const handle = await waitByID(`${genesetName}:geneset-name`);
+
+  const result = await handle.evaluate((node) => {
+    return node.getAttribute("aria-label");
+  });
+
+  return expect(result).toBe(genesetName);
+}
+
+/* 
+
+  GENE
+
+*/
+
+export async function addGeneToSet(genesetName, geneToAddToSet) {
+  const submitButton = `${genesetName}:submit-gene`;
+
+  await clickOn(`${genesetName}:add-new-gene-to-geneset`);
+  await typeInto("add-genes", geneToAddToSet);
+  await clickOn(submitButton);
+}
+
+export async function removeGene(geneSymbol) {
+  const targetId = `delete-from-geneset:${geneSymbol}`;
+
+  await clickOn(targetId);
+
+  await waitByClass("autosave-complete");
+}
+
+export async function assertGeneExistsInGeneset(geneSymbol) {
+  const handle = await waitByID(`${geneSymbol}:gene-label`);
+
+  const result = await handle.evaluate((node) => {
+    return node.getAttribute("aria-label");
+  });
+
+  return expect(result).toBe(geneSymbol);
+}
+
+export async function assertGeneDoesNotExist(geneSymbol) {
+  const result = await isElementPresent(getTestId(`${geneSymbol}:gene-label`));
+
+  await expect(result).toBe(false);
+}
+
+export async function expandGene(geneSymbol) {
+  await clickOn(`maximize-${geneSymbol}`);
+}
+
+/* 
+
+  CATEGORY 
+
+*/
+
 export async function duplicateCategory(categoryName) {
  await clickOn("open-annotation-dialog");

@@ -0,0 +1,105 @@
+export const diffexpPop1Genes = [
+  "CD79A",
+  "HLA-DRB1",
+  "HLA-DQA1",
+  "HLA-DPB1",
+  "HLA-DQB1",
+  "HLA-DPA1",
+  "MS4A1",
+  "LTB",
+  "CD79B",
+  "CD37",
+  "HLA-DMA",
+  "TCL1A",
+  "LINC00926",
+  "HLA-DMB",
+  "HVCN1",
+  "EAF2",
+  "FCRLA",
+  "IRF8",
+  "PKIG",
+  "P2RX5",
+  "HLA-DOB",
+  "SPIB",
+  "BLNK",
+  "SWAP70",
+  "PNOC",
+  "CD19",
+  "SMIM14",
+  "CD72",
+  "KIAA0125",
+  "IGLL5",
+  "ARHGAP24",
+  "COTL1",
+  "C16orf74",
+  "BTK",
+  "SNX29P2",
+  "ADAM28",
+  "FCGR2B",
+  "PLD4",
+  "PPP1R14A",
+  "MZB1",
+  "KIAA0040",
+  "PHACTR1",
+  "FCRL2",
+  "RIC3",
+  "P2RY10",
+  "SCPEP1",
+  "DRAM2",
+  "RP5-887A10.1",
+  "CD82",
+  "GPX1",
+];
+
+export const diffexpPop2Genes = [
+  "NKG7",
+  "GZMB",
+  "CTSW",
+  "PRF1",
+  "GNLY",
+  "GZMA",
+  "CST7",
+  "FGFBP2",
+  "SRGN",
+  "CD247",
+  "FCGR3A",
+  "TYROBP",
+  "FCER1G",
+  "ID2",
+  "SPON2",
+  "CCL4",
+  "CCL5",
+  "GZMH",
+  "GIMAP7",
+  "CLIC3",
+  "HOPX",
+  "XCL2",
+  "LGALS1",
+  "IGFBP7",
+  "AKR1C3",
+  "IL32",
+  "EFHD2",
+  "PRSS23",
+  "TTC38",
+  "ZAP70",
+  "S1PR5",
+  "SAMD3",
+  "GIMAP4",
+  "CCL3",
+  "ABI3",
+  "XCL1",
+  "S100A6",
+  "UBB",
+  "GPR56",
+  "PDIA3",
+  "S100A11",
+  "APOBEC3G",
+  "HAVCR2",
+  "PLEKHF1",
+  "LITAF",
+  "ARPC5L",
+  "PTGDR",
+  "PRMT2",
+  "GSTP1",
+  "FCRL6",
+];
@@ -12,6 +12,7 @@ import {
  getTestId,
  getTestClass,
  getAllByClass,
+  getOneElementInnerHTML,
 } from "./puppeteerUtils";

 import {
@@ -27,6 +28,21 @@ import {
  renameLabel,
  subset,
  duplicateCategory,
+  createGeneset,
+  deleteGeneset,
+  assertGenesetExists,
+  assertGenesetDoesNotExist,
+  getCellSetCount,
+  expandGeneset,
+  editGenesetName,
+  addGeneToSet,
+  assertGeneExistsInGeneset,
+  removeGene,
+  assertGeneDoesNotExist,
+  expandGene,
+  colorByGeneset,
+  assertColorLegendLabel,
+  colorByGene,
 } from "./cellxgeneActions";

 const data = datasets[DATASET];
@@ -34,12 +50,40 @@ const data = datasets[DATASET];
 const perTestCategoryName = "TEST-CATEGORY";
 const perTestLabelName = "TEST-LABEL";

+// geneset CRUD
+const genesetToDeleteName = "geneset_to_delete";
+const preExistingGenesetName = "fifth_dataset";
+const meanExpressionBrushGenesetName = "second_gene_set";
+const meanExpressionBrushCellsSelected = "557";
+const subsetMeanExpressionBrushCellsSelected = "452";
+
+// initial text, the text we type in, the result
+const editableGenesetName = "geneset_to_edit";
+const editText = "_111";
+const newGenesetName = "geneset_to_edit_111";
+
+// add gene to set
+const geneToAddToSet = "RER1";
+const setToAddGeneTo = "fill_this_geneset";
+
+// remove gene from set
+const geneToRemove = "SIK1";
+const setToRemoveFrom = "empty_this_geneset";
+
+// brush a gene
+const geneToBrushAndColorBy = "SIK1";
+const brushThisGeneGeneset = "brush_this_gene";
+const geneBrushedCellCount = "109";
+const subsetGeneBrushedCellCount = "96";
+
 async function setup(config) {
  await goToPage(appUrlBase);

-  // setup the test fixtures
-  await createCategory(perTestCategoryName);
-  await createLabel(perTestCategoryName, perTestLabelName);
+  if (config.categoricalAnno) {
+    // setup the test fixtures
+    await createCategory(perTestCategoryName);
+    await createLabel(perTestCategoryName, perTestLabelName);
+  }

  if (config.withSubset) {
    await subset({ x1: 0.1, y1: 0.1, x2: 0.8, y2: 0.8 });
@@ -51,6 +95,166 @@ async function setup(config) {
 describe.each([
  { withSubset: true, tag: "subset" },
  { withSubset: false, tag: "whole" },
+])("geneSET crud operations and interactions", (config) => {
+  test("genesets load from csv", async () => {
+    await setup(config);
+
+    await assertGenesetExists(preExistingGenesetName);
+  });
+  test("brush on geneset mean", async () => {
+    await setup(config);
+
+    await expandGeneset(meanExpressionBrushGenesetName);
+
+    const histBrushableAreaId = `histogram-${meanExpressionBrushGenesetName}-plot-brushable-area`;
+
+    const coords = await calcDragCoordinates(histBrushableAreaId, {
+      x1: 0.25,
+      y1: 0.5,
+      x2: 0.55,
+      y2: 0.5,
+    });
+
+    await drag(histBrushableAreaId, coords.start, coords.end);
+
+    const cellCount = await getCellSetCount(1);
+    if (config.withSubset) {
+      expect(cellCount).toBe(subsetMeanExpressionBrushCellsSelected);
+    } else {
+      expect(cellCount).toBe(meanExpressionBrushCellsSelected);
+    }
+  });
+  test("color by mean expression", async () => {
+    await setup(config);
+
+    await colorByGeneset(meanExpressionBrushGenesetName);
+    await assertColorLegendLabel(meanExpressionBrushGenesetName);
+  });
+  test("diffexp", async () => {
+    if (config.withSubset) return;
+
+    await setup(config);
+
+    // set the two cell sets to b cells vs nk cells
+    await expandCategory(`louvain`);
+    await clickOn(`louvain:category-select`);
+    await clickOn(`categorical-value-select-louvain-B cells`);
+    await clickOn(`cellset-button-1`);
+    await clickOn(`categorical-value-select-louvain-B cells`);
+    await clickOn(`categorical-value-select-louvain-NK cells`);
+    await clickOn(`cellset-button-2`);
+
+    // run diffexp
+    await clickOn(`diffexp-button`);
+    await waitByClass("pop-1-geneset-expand");
+    await expect(page).toClick(getTestClass("pop-1-geneset-expand"));
+
+    await page.waitForFunction(
+      (selector) => !document.querySelector(selector),
+      {},
+      getTestClass("gene-loading-spinner")
+    );
+
+    let genesHTML = await getOneElementInnerHTML(
+      getTestClass("gene-set-genes")
+    );
+
+    expect(genesHTML).toMatchSnapshot();
+
+    await expect(page).toClick(getTestClass("pop-1-geneset-expand"));
+    await expect(page).toClick(getTestClass("pop-2-geneset-expand"));
+
+    await page.waitForFunction(
+      (selector) => !document.querySelector(selector),
+      {},
+      getTestClass("gene-loading-spinner")
+    );
+
+    genesHTML = await getOneElementInnerHTML(getTestClass("gene-set-genes"));
+
+    expect(genesHTML).toMatchSnapshot();
+  });
+  test("create a new geneset", async () => {
+    if (config.withSubset) return;
+
+    await setup(config);
+
+    const genesetName = `test-geneset-foo-123`;
+    await assertGenesetDoesNotExist(genesetName);
+    await createGeneset(genesetName);
+    /* note: as of June 2021, the aria label is in the truncate component which clones the element */
+    await assertGenesetExists(genesetName);
+  });
+  test("edit geneset name", async () => {
+    await setup(config);
+
+    await editGenesetName(editableGenesetName, editText);
+    await assertGenesetExists(newGenesetName);
+  });
+  test("delete a geneset", async () => {
+    if (config.withSubset) return;
+
+    await setup(config);
+
+    await deleteGeneset(genesetToDeleteName);
+  });
+});
+
+describe.each([
+  { withSubset: true, tag: "subset" },
+  { withSubset: false, tag: "whole" },
+])("GENE crud operations and interactions", (config) => {
+  test("add a gene to geneset", async () => {
+    await setup(config);
+
+    await addGeneToSet(setToAddGeneTo, geneToAddToSet);
+    await expandGeneset(setToAddGeneTo);
+    await assertGeneExistsInGeneset(geneToAddToSet);
+  });
+  test("expand gene and brush", async () => {
+    await setup(config);
+
+    await expandGeneset(brushThisGeneGeneset);
+    await expandGene(geneToBrushAndColorBy);
+    const histBrushableAreaId = `histogram-${geneToBrushAndColorBy}-plot-brushable-area`;
+
+    const coords = await calcDragCoordinates(histBrushableAreaId, {
+      x1: 0.25,
+      y1: 0.5,
+      x2: 0.55,
+      y2: 0.5,
+    });
+    await drag(histBrushableAreaId, coords.start, coords.end);
+    const cellCount = await getCellSetCount(1);
+    if (config.withSubset) {
+      expect(cellCount).toBe(subsetGeneBrushedCellCount);
+    } else {
+      expect(cellCount).toBe(geneBrushedCellCount);
+    }
+  });
+  test("color by gene in geneset", async () => {
+    await setup(config);
+
+    await expandGeneset(meanExpressionBrushGenesetName);
+
+    await colorByGene(geneToBrushAndColorBy);
+    await assertColorLegendLabel(geneToBrushAndColorBy);
+  });
+  test("delete gene from geneset", async () => {
+    // We've already deleted the gene
+    if (config.withSubset) return;
+
+    await setup(config);
+
+    await expandGeneset(setToRemoveFrom);
+    await removeGene(geneToRemove);
+    await assertGeneDoesNotExist(geneToRemove);
+  });
+});
+
+describe.each([
+  { withSubset: true, tag: "subset", categoricalAnno: true },
+  { withSubset: false, tag: "whole", categoricalAnno: true },
 ])("annotations", (config) => {
  test("create a category", async () => {
    await setup(config);
@@ -12,7 +12,7 @@ export async function waitByID(testId, props = {}) {
 }

 export async function waitByClass(testClass, props = {}) {
-  await page.waitForSelector(`[data-testclass='${testClass}']`, props);
+  return page.waitForSelector(`[data-testclass='${testClass}']`, props);
 }

 export async function waitForAllByIds(testIds) {