mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-30 02:58:12 +08:00
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 +1,595 @@
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/*
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Tests included in this file are specific to annotation features
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*/
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import { appUrlBase, DATASET } from "./config";
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import { datasets } from "./data";
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import {
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clickOn,
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goToPage,
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waitByClass,
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waitByID,
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getTestId,
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getTestClass,
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getAllByClass,
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clickOnUntil,
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getOneElementInnerHTML,
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} from "./puppeteerUtils";
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import {
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assertCategoryDoesNotExist,
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calcDragCoordinates,
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createCategory,
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createLabel,
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deleteCategory,
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deleteLabel,
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drag,
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expandCategory,
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renameCategory,
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renameLabel,
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subset,
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duplicateCategory,
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createGeneset,
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deleteGeneset,
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assertGenesetExists,
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assertGenesetDoesNotExist,
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getCellSetCount,
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expandGeneset,
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editGenesetName,
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addGeneToSet,
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assertGeneExistsInGeneset,
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removeGene,
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assertGeneDoesNotExist,
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expandGene,
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colorByGeneset,
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assertColorLegendLabel,
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colorByGene,
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} from "./cellxgeneActions";
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const data = datasets[DATASET];
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const perTestCategoryName = "TEST-CATEGORY";
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const perTestLabelName = "TEST-LABEL";
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// geneset CRUD
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const genesetToDeleteName = "geneset_to_delete";
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const preExistingGenesetName = "fifth_dataset";
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const meanExpressionBrushGenesetName = "second_gene_set";
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const meanExpressionBrushCellsSelected = "557";
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const subsetMeanExpressionBrushCellsSelected = "452";
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// initial text, the text we type in, the result
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const editableGenesetName = "geneset_to_edit";
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const editText = "_111";
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const newGenesetName = "geneset_to_edit_111";
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// add gene to set
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const geneToAddToSet = "RER1";
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const setToAddGeneTo = "fill_this_geneset";
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// remove gene from set
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const geneToRemove = "SIK1";
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const setToRemoveFrom = "empty_this_geneset";
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// brush a gene
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const geneToBrushAndColorBy = "SIK1";
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const brushThisGeneGeneset = "brush_this_gene";
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const geneBrushedCellCount = "109";
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const subsetGeneBrushedCellCount = "96";
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const genesetDescriptionID =
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"geneset-description-tooltip-fourth_gene_set: fourth description";
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const genesetDescriptionString = "fourth_gene_set: fourth description";
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const genesetToCheckForDescription = "fourth_gene_set";
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async function setup(config) {
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await goToPage(appUrlBase);
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if (config.categoricalAnno) {
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// setup the test fixtures
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await createCategory(perTestCategoryName);
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await createLabel(perTestCategoryName, perTestLabelName);
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}
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if (config.withSubset) {
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await subset({ x1: 0.1, y1: 0.1, x2: 0.8, y2: 0.8 });
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}
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await waitByClass("autosave-complete");
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}
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describe.each([
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{ withSubset: true, tag: "subset" },
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{ withSubset: false, tag: "whole" },
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])("geneSET crud operations and interactions", (config) => {
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test("genesets load from csv", async () => {
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await setup(config);
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await assertGenesetExists(preExistingGenesetName);
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});
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test("brush on geneset mean", async () => {
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await setup(config);
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await expandGeneset(meanExpressionBrushGenesetName);
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const histBrushableAreaId = `histogram-${meanExpressionBrushGenesetName}-plot-brushable-area`;
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const coords = await calcDragCoordinates(histBrushableAreaId, {
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x1: 0.25,
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y1: 0.5,
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x2: 0.55,
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y2: 0.5,
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});
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await drag(histBrushableAreaId, coords.start, coords.end);
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const cellCount = await getCellSetCount(1);
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if (config.withSubset) {
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expect(cellCount).toBe(subsetMeanExpressionBrushCellsSelected);
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} else {
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expect(cellCount).toBe(meanExpressionBrushCellsSelected);
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}
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});
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test("color by mean expression", async () => {
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await setup(config);
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await colorByGeneset(meanExpressionBrushGenesetName);
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await assertColorLegendLabel(meanExpressionBrushGenesetName);
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});
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test("diffexp", async () => {
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if (config.withSubset) return;
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await setup(config);
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// set the two cell sets to b cells vs nk cells
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await expandCategory(`louvain`);
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await clickOn(`louvain:category-select`);
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await clickOn(`categorical-value-select-louvain-B cells`);
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await clickOn(`cellset-button-1`);
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await clickOn(`categorical-value-select-louvain-B cells`);
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await clickOn(`categorical-value-select-louvain-NK cells`);
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await clickOn(`cellset-button-2`);
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// run diffexp
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await clickOn(`diffexp-button`);
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await waitByClass("pop-1-geneset-expand");
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await expect(page).toClick(getTestClass("pop-1-geneset-expand"));
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await page.waitForFunction(
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(selector) => !document.querySelector(selector),
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{},
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getTestClass("gene-loading-spinner")
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);
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let genesHTML = await getOneElementInnerHTML(
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getTestClass("gene-set-genes")
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);
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expect(genesHTML).toMatchSnapshot();
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await expect(page).toClick(getTestClass("pop-1-geneset-expand"));
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await expect(page).toClick(getTestClass("pop-2-geneset-expand"));
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await page.waitForFunction(
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(selector) => !document.querySelector(selector),
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{},
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getTestClass("gene-loading-spinner")
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);
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genesHTML = await getOneElementInnerHTML(getTestClass("gene-set-genes"));
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expect(genesHTML).toMatchSnapshot();
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});
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test("create a new geneset and undo/redo", async () => {
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if (config.withSubset) return;
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await setup(config);
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const genesetName = `test-geneset-foo-123`;
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await assertGenesetDoesNotExist(genesetName);
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await createGeneset(genesetName);
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/* note: as of June 2021, the aria label is in the truncate component which clones the element */
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await assertGenesetExists(genesetName);
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await clickOn("undo");
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await assertGenesetDoesNotExist(genesetName);
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await clickOn("redo");
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await assertGenesetExists(genesetName);
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});
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test("edit geneset name and undo/redo", async () => {
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await setup(config);
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await editGenesetName(editableGenesetName, editText);
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await assertGenesetExists(newGenesetName);
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await clickOn("undo");
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await assertGenesetExists(editableGenesetName);
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await clickOn("redo");
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await assertGenesetExists(newGenesetName);
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});
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test("delete a geneset and undo/redo", async () => {
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if (config.withSubset) return;
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await setup(config);
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await deleteGeneset(genesetToDeleteName);
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await clickOn("undo");
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await assertGenesetExists(genesetToDeleteName);
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await clickOn("redo");
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await assertGenesetDoesNotExist(genesetToDeleteName);
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});
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test("geneset description", async () => {
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if (config.withSubset) return;
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await setup(config);
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await clickOnUntil(
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`${genesetToCheckForDescription}:geneset-expand`,
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async () => {
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expect(page).toMatchElement(getTestId(genesetDescriptionID), {
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text: genesetDescriptionString,
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});
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}
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);
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});
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});
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describe.each([
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{ withSubset: true, tag: "subset" },
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{ withSubset: false, tag: "whole" },
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])("GENE crud operations and interactions", (config) => {
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test("add a gene to geneset and undo/redo", async () => {
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await setup(config);
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await addGeneToSet(setToAddGeneTo, geneToAddToSet);
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await expandGeneset(setToAddGeneTo);
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await assertGeneExistsInGeneset(geneToAddToSet);
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await clickOn("undo");
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await assertGeneDoesNotExist(geneToAddToSet);
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await clickOn("redo");
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await assertGeneExistsInGeneset(geneToAddToSet);
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});
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test("expand gene and brush", async () => {
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await setup(config);
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await expandGeneset(brushThisGeneGeneset);
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await expandGene(geneToBrushAndColorBy);
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const histBrushableAreaId = `histogram-${geneToBrushAndColorBy}-plot-brushable-area`;
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const coords = await calcDragCoordinates(histBrushableAreaId, {
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x1: 0.25,
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y1: 0.5,
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x2: 0.55,
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y2: 0.5,
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});
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await drag(histBrushableAreaId, coords.start, coords.end);
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const cellCount = await getCellSetCount(1);
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if (config.withSubset) {
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expect(cellCount).toBe(subsetGeneBrushedCellCount);
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} else {
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expect(cellCount).toBe(geneBrushedCellCount);
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}
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});
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test("color by gene in geneset", async () => {
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await setup(config);
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await expandGeneset(meanExpressionBrushGenesetName);
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await colorByGene(geneToBrushAndColorBy);
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await assertColorLegendLabel(geneToBrushAndColorBy);
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});
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test("delete gene from geneset and undo/redo", async () => {
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// We've already deleted the gene
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if (config.withSubset) return;
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await setup(config);
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await expandGeneset(setToRemoveFrom);
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await removeGene(geneToRemove);
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await assertGeneDoesNotExist(geneToRemove);
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await clickOn("undo");
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await assertGeneExistsInGeneset(geneToRemove);
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await clickOn("redo");
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await assertGeneDoesNotExist(geneToRemove);
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});
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});
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describe.each([
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{ withSubset: true, tag: "subset", categoricalAnno: true },
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{ withSubset: false, tag: "whole", categoricalAnno: true },
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])("annotations", (config) => {
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test("create a category", async () => {
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await setup(config);
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const categoryName = `category-created-${config.tag}`;
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await assertCategoryDoesNotExist(categoryName);
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await createCategory(categoryName);
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await assertCategoryExists(categoryName);
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});
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test("delete a category", async () => {
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await setup(config);
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await deleteCategory(perTestCategoryName);
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await assertCategoryDoesNotExist(perTestCategoryName);
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});
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test("rename a category", async () => {
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await setup(config);
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const newCategoryName = `NEW-${config.tag}`;
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await renameCategory(perTestCategoryName, newCategoryName);
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await assertCategoryDoesNotExist(perTestCategoryName);
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await assertCategoryExists(newCategoryName);
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});
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test("create a label", async () => {
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await setup(config);
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const labelName = `new-label-${config.tag}`;
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await assertLabelDoesNotExist(perTestCategoryName, labelName);
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await createLabel(perTestCategoryName, labelName);
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await assertLabelExists(perTestCategoryName, labelName);
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});
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test("delete a label", async () => {
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await setup(config);
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await deleteLabel(perTestCategoryName, perTestLabelName);
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await assertLabelDoesNotExist(perTestCategoryName, perTestLabelName);
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});
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test("rename a label", async () => {
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await setup(config);
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const newLabelName = "my-cool-new-label";
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await assertLabelDoesNotExist(perTestCategoryName, newLabelName);
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await renameLabel(perTestCategoryName, perTestLabelName, newLabelName);
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await assertLabelDoesNotExist(perTestCategoryName, perTestLabelName);
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await assertLabelExists(perTestCategoryName, newLabelName);
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});
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test("check cell count for a label loaded from file", async () => {
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await setup(config);
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const duplicateCategoryName = "duplicate";
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await duplicateCategory(duplicateCategoryName);
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await page.reload({ waitUntil: ["networkidle0", "domcontentloaded"] });
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const firstCategoryExpandIcon = await expect(page).toMatchElement(
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getTestClass("category-expand")
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);
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await firstCategoryExpandIcon.click();
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const expectedCategoryRow = await expect(page).toMatchElement(
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getTestClass("categorical-row")
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);
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const expectedLabelName = await getInnerText(
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expectedCategoryRow,
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"categorical-value"
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);
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const expectedLabelCount = await getInnerText(
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expectedCategoryRow,
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"categorical-value-count"
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);
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await expandCategory(duplicateCategoryName);
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const expectedCategory = await expect(page).toMatchElement(
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getTestClass("category")
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);
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const actualCategoryRow = await expect(expectedCategory).toMatchElement(
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getTestClass("categorical-row")
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);
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const actualLabelName = await getInnerText(
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actualCategoryRow,
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"categorical-value"
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);
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const actualLabelCount = await getInnerText(
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actualCategoryRow,
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"categorical-value-count"
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);
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expect(actualLabelName).toBe(expectedLabelName);
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expect(actualLabelCount).toBe(expectedLabelCount);
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async function getInnerText(element, className) {
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return element.$eval(getTestClass(className), (node) => node?.innerText);
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}
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});
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test("assign cells to a label", async () => {
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await setup(config);
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await expandCategory(perTestCategoryName);
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const lassoSelection = await calcDragCoordinates(
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"layout-graph",
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data.categoryLabel.lasso["coordinates-as-percent"]
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);
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await drag("layout-graph", lassoSelection.start, lassoSelection.end, true);
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await waitByID("lasso-element", { visible: true });
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await clickOn(`${perTestCategoryName}:${perTestLabelName}:see-actions`);
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await clickOn(
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`${perTestCategoryName}:${perTestLabelName}:add-current-selection-to-this-label`
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);
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const result = await waitByID(
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`categorical-value-count-${perTestCategoryName}-${perTestLabelName}`
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);
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expect(await result.evaluate((node) => node.innerText)).toBe(
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data.categoryLabel.newCount.bySubsetConfig[config.withSubset]
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);
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});
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test("undo/redo category creation", async () => {
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await setup(config);
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const categoryName = `category-created-undo-${config.tag}`;
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await assertCategoryDoesNotExist(categoryName);
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await createCategory(categoryName);
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await assertCategoryExists(categoryName);
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await clickOn("undo");
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await assertCategoryDoesNotExist(categoryName);
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await clickOn("redo");
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await assertCategoryExists(categoryName);
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});
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test("undo/redo category deletion", async () => {
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await setup(config);
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const categoryName = `category-deleted-undo-${config.tag}`;
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await createCategory(categoryName);
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await assertCategoryExists(categoryName);
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await deleteCategory(categoryName);
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await assertCategoryDoesNotExist(categoryName);
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await clickOn("undo");
|
||||
await assertCategoryExists(categoryName);
|
||||
await clickOn("redo");
|
||||
await assertCategoryDoesNotExist(categoryName);
|
||||
});
|
||||
|
||||
test("undo/redo category rename", async () => {
|
||||
await setup(config);
|
||||
|
||||
const newCategoryName = `category-renamed-undo-${config.tag}`;
|
||||
|
||||
await assertCategoryDoesNotExist(newCategoryName);
|
||||
await renameCategory(perTestCategoryName, newCategoryName);
|
||||
await assertCategoryExists(newCategoryName);
|
||||
await assertCategoryDoesNotExist(perTestCategoryName);
|
||||
await clickOn("undo");
|
||||
await assertCategoryExists(perTestCategoryName);
|
||||
await assertCategoryDoesNotExist(newCategoryName);
|
||||
await clickOn("redo");
|
||||
await assertCategoryExists(newCategoryName);
|
||||
await assertCategoryDoesNotExist(perTestCategoryName);
|
||||
});
|
||||
|
||||
test("undo/redo label creation", async () => {
|
||||
await setup(config);
|
||||
|
||||
const labelName = `label-created-undo-${config.tag}`;
|
||||
|
||||
await assertLabelDoesNotExist(perTestCategoryName, labelName);
|
||||
await createLabel(perTestCategoryName, labelName);
|
||||
await assertLabelExists(perTestCategoryName, labelName);
|
||||
await clickOn("undo");
|
||||
await assertLabelDoesNotExist(perTestCategoryName);
|
||||
await clickOn("redo");
|
||||
await assertLabelExists(perTestCategoryName, labelName);
|
||||
});
|
||||
|
||||
test("undo/redo label deletion", async () => {
|
||||
await setup(config);
|
||||
|
||||
await deleteLabel(perTestCategoryName, perTestLabelName);
|
||||
await assertLabelDoesNotExist(perTestCategoryName);
|
||||
await clickOn("undo");
|
||||
await assertLabelExists(perTestCategoryName, perTestLabelName);
|
||||
await clickOn("redo");
|
||||
await assertLabelDoesNotExist(perTestCategoryName);
|
||||
});
|
||||
|
||||
test("undo/redo label rename", async () => {
|
||||
await setup(config);
|
||||
|
||||
const newLabelName = `label-renamed-undo-${config.tag}`;
|
||||
|
||||
await assertLabelDoesNotExist(perTestCategoryName, newLabelName);
|
||||
await renameLabel(perTestCategoryName, perTestLabelName, newLabelName);
|
||||
await assertLabelExists(perTestCategoryName, newLabelName);
|
||||
await assertLabelDoesNotExist(perTestCategoryName, perTestLabelName);
|
||||
await clickOn("undo");
|
||||
await assertLabelExists(perTestCategoryName, perTestLabelName);
|
||||
await assertLabelDoesNotExist(perTestCategoryName, newLabelName);
|
||||
await clickOn("redo");
|
||||
await assertLabelExists(perTestCategoryName, newLabelName);
|
||||
await assertLabelDoesNotExist(perTestCategoryName, perTestLabelName);
|
||||
});
|
||||
|
||||
test("stacked bar graph renders", async () => {
|
||||
await setup(config);
|
||||
|
||||
await expandCategory(perTestCategoryName);
|
||||
|
||||
await clickOn(`colorby-louvain`);
|
||||
|
||||
const labels = await getAllByClass("categorical-row");
|
||||
|
||||
const result = await Promise.all(
|
||||
labels.map((label) => page.evaluate((element) => element.outerHTML, label))
|
||||
);
|
||||
|
||||
expect(result).toMatchSnapshot();
|
||||
});
|
||||
|
||||
test("truncate midpoint whitespace", async () => {
|
||||
await setup(config);
|
||||
const newLabelName = "123 456";
|
||||
await renameLabel(perTestCategoryName, perTestLabelName, newLabelName);
|
||||
const value = await waitByID(
|
||||
`categorical-value-${perTestCategoryName}-${newLabelName}`
|
||||
);
|
||||
const result = await page.evaluate((elem) => elem.outerHTML, value);
|
||||
expect(result).toMatchSnapshot();
|
||||
});
|
||||
|
||||
test("truncate single character", async () => {
|
||||
await setup(config);
|
||||
const newLabelName = "T";
|
||||
await renameLabel(perTestCategoryName, perTestLabelName, newLabelName);
|
||||
const value = await waitByID(
|
||||
`categorical-value-${perTestCategoryName}-${newLabelName}`
|
||||
);
|
||||
const result = await page.evaluate((elem) => elem.outerHTML, value);
|
||||
expect(result).toMatchSnapshot();
|
||||
});
|
||||
|
||||
async function assertCategoryExists(categoryName) {
|
||||
const handle = await waitByID(`${categoryName}:category-label`);
|
||||
|
||||
const result = await handle.evaluate((node) =>
|
||||
node.getAttribute("aria-label")
|
||||
);
|
||||
|
||||
return expect(result).toBe(categoryName);
|
||||
}
|
||||
|
||||
async function assertLabelExists(categoryName, labelName) {
|
||||
await expect(page).toMatchElement(
|
||||
getTestId(`${categoryName}:category-expand`)
|
||||
);
|
||||
|
||||
await expandCategory(categoryName);
|
||||
|
||||
const previous = await waitByID(
|
||||
`categorical-value-${categoryName}-${labelName}`
|
||||
);
|
||||
|
||||
expect(
|
||||
await previous.evaluate((node) => node.getAttribute("aria-label"))
|
||||
).toBe(labelName);
|
||||
}
|
||||
|
||||
async function assertLabelDoesNotExist(categoryName, labelName) {
|
||||
await expandCategory(categoryName);
|
||||
const result = await page.$(
|
||||
`[data-testid='categorical-value-${categoryName}-${labelName}']`
|
||||
);
|
||||
expect(result).toBeNull();
|
||||
}
|
||||
});
|
||||
Reference in New Issue
Block a user