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TS migration. #2288. (#2328)

Browse Source 
* Added TS. Updated build and linting config. Added types.

* [ts-migrate][.] Rename files from JS/JSX to TS/TSX

Co-authored-by: ts-migrate <>

* [ts-migrate][.] Run TS Migrate

Co-authored-by: ts-migrate <>

* Corrected files mangled by ts-migrate.

* Updated lint config, minor linting.

* Re-enabled Husky.

* Updated tests and config.

* Reverted webpack devtool config.

* Removed obsolete snapshots.

* Added annotations snap.

* Updated tsconfig includes wrt linting.

* Removed ts-migrate.

Co-authored-by: Timmy Huang <tihuan@users.noreply.github.com>
This commit is contained in:
Mim Hastie
2021-07-26 20:18:17 +00:00
committed by GitHub
co-authored by ts-migrate Timmy Huang
parent 7328cbdbd5
commit 934cc5c69b
206 changed files with 4719 additions and 2085 deletions
Download Patch File Download Diff File Expand all files Collapse all files
client/__tests__/e2e/__snapshots__/e2e.test.js.snap → client/__tests__/e2e/__snapshots__/e2e.test.ts.snap
View File
client/__tests__/e2e/__snapshots__/e2eAnnotations.test.js.snap → client/__tests__/e2e/__snapshots__/e2eAnnotations.test.ts.snap
View File
client/__tests__/e2e/cellxgeneActions.js → client/__tests__/e2e/cellxgeneActions.ts
+76 -42
View File
@@ -18,12 +18,17 @@ import {
import { appUrlBase, TEST_EMAIL, TEST_PASSWORD } from "./config";
export async function drag(testId, start, end, lasso = false) {
export async function drag(testId: any, start: any, end: any, lasso = false) {
const layout = await waitByID(testId);
// @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
const elBox = await layout.boxModel();
// @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
const x1 = elBox.content[0].x + start.x;
// @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
const x2 = elBox.content[0].x + end.x;
// @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
const y1 = elBox.content[0].y + start.y;
// @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
const y2 = elBox.content[0].y + end.y;
await page.mouse.move(x1, y1);
await page.mouse.down();
@@ -38,7 +43,7 @@ export async function drag(testId, start, end, lasso = false) {
await page.mouse.up();
}
export async function clickOnCoordinate(testId, coord) {
export async function clickOnCoordinate(testId: any, coord: any) {
const layout = await expect(page).toMatchElement(getTestId(testId));
const elBox = await layout.boxModel();
@@ -51,11 +56,12 @@ export async function clickOnCoordinate(testId, coord) {
await page.mouse.click(x, y);
}
export async function getAllHistograms(testclass, testIds) {
const histTestIds = testIds.map((tid) => `histogram-${tid}`);
export async function getAllHistograms(testclass: any, testIds: any) {
const histTestIds = testIds.map((tid: any) => `histogram-${tid}`);
// these load asynchronously, so we need to wait for each histogram individually,
// and they may be quite slow in some cases.
// @ts-expect-error ts-migrate(2554) FIXME: Expected 1 arguments, but got 2.
await waitForAllByIds(histTestIds, { timeout: 4 * 60 * 1000 });
const allHistograms = await getAllByClass(testclass);
@@ -71,7 +77,7 @@ export async function getAllHistograms(testclass, testIds) {
return testIDs.map((id) => id.replace(/^histogram-/, ""));
}
export async function getAllCategoriesAndCounts(category) {
export async function getAllCategoriesAndCounts(category: any) {
// these load asynchronously, so we have to wait for the specific category.
await waitByID(`category-${category}`);
@@ -80,13 +86,14 @@ export async function getAllCategoriesAndCounts(category) {
(rows) =>
Object.fromEntries(
rows.map((row) => {
// @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
const cat = row
.querySelector("[data-testclass='categorical-value']")
.getAttribute("aria-label");
const count = row.querySelector(
const count = (row.querySelector(
"[data-testclass='categorical-value-count']"
).innerText;
) as any).innerText;
return [cat, count];
})
@@ -94,12 +101,12 @@ export async function getAllCategoriesAndCounts(category) {
);
}
export async function getCellSetCount(num) {
export async function getCellSetCount(num: any) {
await clickOn(`cellset-button-${num}`);
return getOneElementInnerText(`[data-testid='cellset-count-${num}']`);
}
export async function resetCategory(category) {
export async function resetCategory(category: any) {
const checkboxId = `${category}:category-select`;
await waitByID(checkboxId);
const checkedPseudoclass = await page.$eval(
@@ -110,6 +117,7 @@ export async function resetCategory(category) {
const categoryRow = await waitByID(`${category}:category-expand`);
// @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
const isExpanded = await categoryRow.$(
"[data-testclass='category-expand-is-expanded']"
);
@@ -117,16 +125,26 @@ export async function resetCategory(category) {
if (isExpanded) await clickOn(`${category}:category-expand`);
}
export async function calcCoordinate(testId, xAsPercent, yAsPercent) {
export async function calcCoordinate(
testId: any,
xAsPercent: any,
yAsPercent: any
) {
const el = await waitByID(testId);
// @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
const size = await el.boxModel();
return {
// @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
x: Math.floor(size.width * xAsPercent),
// @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
y: Math.floor(size.height * yAsPercent),
};
}
export async function calcDragCoordinates(testId, coordinateAsPercent) {
export async function calcDragCoordinates(
testId: any,
coordinateAsPercent: any
) {
return {
start: await calcCoordinate(
testId,
@@ -141,7 +159,7 @@ export async function calcDragCoordinates(testId, coordinateAsPercent) {
};
}
export async function selectCategory(category, values, reset = true) {
export async function selectCategory(category: any, values: any, reset = true) {
if (reset) await resetCategory(category);
await clickOn(`${category}:category-expand`);
@@ -152,8 +170,9 @@ export async function selectCategory(category, values, reset = true) {
}
}
export async function expandCategory(category) {
export async function expandCategory(category: any) {
const expand = await waitByID(`${category}:category-expand`);
// @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
const notExpanded = await expand.$(
"[data-testclass='category-expand-is-not-expanded']"
);
@@ -167,7 +186,7 @@ export async function clip(min = 0, max = 100) {
await clickOn("clip-commit");
}
export async function createCategory(categoryName) {
export async function createCategory(categoryName: any) {
await clickOnUntil("open-annotation-dialog", async () => {
await expect(page).toMatchElement(getTestId("new-category-name"));
});
@@ -182,17 +201,18 @@ export async function createCategory(categoryName) {
*/
export async function colorByGeneset(genesetName) {
export async function colorByGeneset(genesetName: any) {
await clickOn(`${genesetName}:colorby-entire-geneset`);
}
export async function colorByGene(gene) {
export async function colorByGene(gene: any) {
await clickOn(`colorby-${gene}`);
}
export async function assertColorLegendLabel(label) {
export async function assertColorLegendLabel(label: any) {
const handle = await waitByID("continuous_legend_color_by_label");
// @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
const result = await handle.evaluate((node) => {
return node.getAttribute("aria-label");
});
@@ -200,15 +220,16 @@ export async function assertColorLegendLabel(label) {
return expect(result).toBe(label);
}
export async function expandGeneset(genesetName) {
export async function expandGeneset(genesetName: any) {
const expand = await waitByID(`${genesetName}:geneset-expand`);
// @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
const notExpanded = await expand.$(
"[data-testclass='geneset-expand-is-not-expanded']"
);
if (notExpanded) await clickOn(`${genesetName}:geneset-expand`);
}
export async function createGeneset(genesetName) {
export async function createGeneset(genesetName: any) {
await clickOnUntil("open-create-geneset-dialog", async () => {
await expect(page).toMatchElement(getTestId("create-geneset-input"));
});
@@ -218,7 +239,7 @@ export async function createGeneset(genesetName) {
await waitByClass("autosave-complete");
}
export async function editGenesetName(genesetName, editText) {
export async function editGenesetName(genesetName: any, editText: any) {
const editButton = `${genesetName}:edit-genesetName-mode`;
const submitButton = `${genesetName}:submit-geneset`;
await clickOnUntil(`${genesetName}:see-actions`, async () => {
@@ -229,7 +250,7 @@ export async function editGenesetName(genesetName, editText) {
await clickOn(submitButton);
}
export async function deleteGeneset(genesetName) {
export async function deleteGeneset(genesetName: any) {
const targetId = `${genesetName}:delete-geneset`;
await clickOnUntil(`${genesetName}:see-actions`, async () => {
@@ -242,16 +263,18 @@ export async function deleteGeneset(genesetName) {
await waitByClass("autosave-complete");
}
export async function assertGenesetDoesNotExist(genesetName) {
export async function assertGenesetDoesNotExist(genesetName: any) {
// @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1.
const result = await isElementPresent(
getTestId(`${genesetName}:geneset-name`)
);
await expect(result).toBe(false);
}
export async function assertGenesetExists(genesetName) {
export async function assertGenesetExists(genesetName: any) {
const handle = await waitByID(`${genesetName}:geneset-name`);
// @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
const result = await handle.evaluate((node) => {
return node.getAttribute("aria-label");
});
@@ -265,7 +288,7 @@ export async function assertGenesetExists(genesetName) {
*/
export async function addGeneToSet(genesetName, geneToAddToSet) {
export async function addGeneToSet(genesetName: any, geneToAddToSet: any) {
const submitButton = `${genesetName}:submit-gene`;
await clickOn(`${genesetName}:add-new-gene-to-geneset`);
@@ -273,7 +296,7 @@ export async function addGeneToSet(genesetName, geneToAddToSet) {
await clickOn(submitButton);
}
export async function removeGene(geneSymbol) {
export async function removeGene(geneSymbol: any) {
const targetId = `delete-from-geneset:${geneSymbol}`;
await clickOn(targetId);
@@ -281,9 +304,10 @@ export async function removeGene(geneSymbol) {
await waitByClass("autosave-complete");
}
export async function assertGeneExistsInGeneset(geneSymbol) {
export async function assertGeneExistsInGeneset(geneSymbol: any) {
const handle = await waitByID(`${geneSymbol}:gene-label`);
// @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
const result = await handle.evaluate((node) => {
return node.getAttribute("aria-label");
});
@@ -291,13 +315,14 @@ export async function assertGeneExistsInGeneset(geneSymbol) {
return expect(result).toBe(geneSymbol);
}
export async function assertGeneDoesNotExist(geneSymbol) {
export async function assertGeneDoesNotExist(geneSymbol: any) {
// @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1.
const result = await isElementPresent(getTestId(`${geneSymbol}:gene-label`));
await expect(result).toBe(false);
}
export async function expandGene(geneSymbol) {
export async function expandGene(geneSymbol: any) {
await clickOn(`maximize-${geneSymbol}`);
}
@@ -307,7 +332,7 @@ export async function expandGene(geneSymbol) {
*/
export async function duplicateCategory(categoryName) {
export async function duplicateCategory(categoryName: any) {
await clickOn("open-annotation-dialog");
await typeInto("new-category-name", categoryName);
@@ -333,7 +358,10 @@ export async function duplicateCategory(categoryName) {
await waitByClass("autosave-complete");
}
export async function renameCategory(oldCategoryName, newCategoryName) {
export async function renameCategory(
oldCategoryName: any,
newCategoryName: any
) {
await clickOn(`${oldCategoryName}:see-actions`);
await clickOn(`${oldCategoryName}:edit-category-mode`);
await clearInputAndTypeInto(
@@ -343,7 +371,7 @@ export async function renameCategory(oldCategoryName, newCategoryName) {
await clickOn(`${oldCategoryName}:submit-category-edit`);
}
export async function deleteCategory(categoryName) {
export async function deleteCategory(categoryName: any) {
const targetId = `${categoryName}:delete-category`;
await clickOnUntil(`${categoryName}:see-actions`, async () => {
@@ -352,10 +380,11 @@ export async function deleteCategory(categoryName) {
await clickOn(targetId);
// @ts-expect-error ts-migrate(2554) FIXME: Expected 1 arguments, but got 0.
await assertCategoryDoesNotExist();
}
export async function createLabel(categoryName, labelName) {
export async function createLabel(categoryName: any, labelName: any) {
/**
* (thuang): This explicit wait is needed, since currently showing
* the modal again quickly after the previous action dismissing the
@@ -380,13 +409,17 @@ export async function createLabel(categoryName, labelName) {
await clickOn(`${categoryName}:submit-label`);
}
export async function deleteLabel(categoryName, labelName) {
export async function deleteLabel(categoryName: any, labelName: any) {
await expandCategory(categoryName);
await clickOn(`${categoryName}:${labelName}:see-actions`);
await clickOn(`${categoryName}:${labelName}:delete-label`);
}
export async function renameLabel(categoryName, oldLabelName, newLabelName) {
export async function renameLabel(
categoryName: any,
oldLabelName: any,
newLabelName: any
) {
await expandCategory(categoryName);
await clickOn(`${categoryName}:${oldLabelName}:see-actions`);
await clickOn(`${categoryName}:${oldLabelName}:edit-label`);
@@ -397,13 +430,13 @@ export async function renameLabel(categoryName, oldLabelName, newLabelName) {
await clickOn(`${categoryName}:${oldLabelName}:submit-label-edit`);
}
export async function addGeneToSearch(geneName) {
export async function addGeneToSearch(geneName: any) {
await typeInto("gene-search", geneName);
await page.keyboard.press("Enter");
await page.waitForSelector(`[data-testid='histogram-${geneName}']`);
}
export async function subset(coordinatesAsPercent) {
export async function subset(coordinatesAsPercent: any) {
// In order to deselect the selection after the subset, make sure we have some clear part
// of the scatterplot we can click on
assert(coordinatesAsPercent.x2 < 0.99 || coordinatesAsPercent.y2 < 0.99);
@@ -417,8 +450,8 @@ export async function subset(coordinatesAsPercent) {
await clickOnCoordinate("layout-graph", clearCoordinate);
}
export async function setSellSet(cellSet, cellSetNum) {
const selections = cellSet.filter((sel) => sel.kind === "categorical");
export async function setSellSet(cellSet: any, cellSetNum: any) {
const selections = cellSet.filter((sel: any) => sel.kind === "categorical");
for (const selection of selections) {
await selectCategory(selection.metadata, selection.values, true);
@@ -427,19 +460,20 @@ export async function setSellSet(cellSet, cellSetNum) {
await getCellSetCount(cellSetNum);
}
export async function runDiffExp(cellSet1, cellSet2) {
export async function runDiffExp(cellSet1: any, cellSet2: any) {
await setSellSet(cellSet1, 1);
await setSellSet(cellSet2, 2);
await clickOn("diffexp-button");
}
export async function bulkAddGenes(geneNames) {
export async function bulkAddGenes(geneNames: any) {
await clickOn("section-bulk-add");
await typeInto("input-bulk-add", geneNames.join(","));
await page.keyboard.press("Enter");
}
export async function assertCategoryDoesNotExist(categoryName) {
export async function assertCategoryDoesNotExist(categoryName: any) {
// @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1.
const result = await isElementPresent(
getTestId(`${categoryName}:category-label`)
);
@@ -480,7 +514,7 @@ export async function logout() {
await waitByID("log-in");
}
async function waitUntilFormFieldStable(selector) {
async function waitUntilFormFieldStable(selector: any) {
const MAX_RETRY = 10;
const WAIT_FOR_MS = 200;
client/__tests__/e2e/config.js → client/__tests__/e2e/config.ts
View File
client/__tests__/e2e/data.js → client/__tests__/e2e/data.ts
View File
client/__tests__/e2e/diffexpGeneSets.js → client/__tests__/e2e/diffexpGeneSets.ts
View File
client/__tests__/e2e/e2e.test.js → client/__tests__/e2e/e2e.test.ts
+7
View File
@@ -58,10 +58,12 @@ describe("metadata loads", () => {
const categories = await getAllCategoriesAndCounts(label);
expect(Object.keys(categories)).toMatchObject(
// @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message
Object.keys(data.categorical[label])
);
expect(Object.values(categories)).toMatchObject(
// @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message
Object.values(data.categorical[label])
);
}
@@ -159,10 +161,12 @@ describe("subset", () => {
const categories = await getAllCategoriesAndCounts(label);
expect(Object.keys(categories)).toMatchObject(
// @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message
Object.keys(data.subset.categorical[label])
);
expect(Object.values(categories)).toMatchObject(
// @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message
Object.values(data.subset.categorical[label])
);
}
@@ -195,6 +199,7 @@ describe("clipping", () => {
test("clip continuous", async () => {
await goToPage(appUrlBase);
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'string' is not assignable to par... Remove this comment to see the full error message
await clip(data.clip.min, data.clip.max);
const histBrushableAreaId = `histogram-${data.clip.metadata}-plot-brushable-area`;
const coords = await calcDragCoordinates(
@@ -254,6 +259,7 @@ describe("centroid labels", () => {
const generatedLabels = await getAllByClass("centroid-label");
// Number of labels generated should be equal to size of the object
expect(generatedLabels).toHaveLength(
// @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message
Object.keys(data.categorical[label]).length
);
}
@@ -275,6 +281,7 @@ describe("graph overlay", () => {
data.pan["coordinates-as-percent"]
);
// @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message
const categoryValue = Object.keys(data.categorical[category])[0];
const initialCoordinates = await getElementCoordinates(
`${categoryValue}-centroid-label`
client/__tests__/e2e/e2eAnnotations.test.js → client/__tests__/e2e/e2eAnnotations.test.ts
+18 -8
View File
@@ -76,7 +76,7 @@ const brushThisGeneGeneset = "brush_this_gene";
const geneBrushedCellCount = "109";
const subsetGeneBrushedCellCount = "96";
async function setup(config) {
async function setup(config: any) {
await goToPage(appUrlBase);
if (config.categoricalAnno) {
@@ -150,7 +150,7 @@ describe.each([
await expect(page).toClick(getTestClass("pop-1-geneset-expand"));
await page.waitForFunction(
(selector) => !document.querySelector(selector),
(selector: any) => !document.querySelector(selector),
{},
getTestClass("gene-loading-spinner")
);
@@ -165,7 +165,7 @@ describe.each([
await expect(page).toClick(getTestClass("pop-2-geneset-expand"));
await page.waitForFunction(
(selector) => !document.querySelector(selector),
(selector: any) => !document.querySelector(selector),
{},
getTestClass("gene-loading-spinner")
);
@@ -362,8 +362,11 @@ describe.each([
expect(actualLabelName).toBe(expectedLabelName);
expect(actualLabelCount).toBe(expectedLabelCount);
async function getInnerText(element, className) {
return element.$eval(getTestClass(className), (node) => node?.innerText);
async function getInnerText(element: any, className: any) {
return element.$eval(
getTestClass(className),
(node: any) => node?.innerText
);
}
});
@@ -388,7 +391,9 @@ describe.each([
`categorical-value-count-${perTestCategoryName}-${perTestLabelName}`
);
// @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
expect(await result.evaluate((node) => node.innerText)).toBe(
// @ts-expect-error ts-migrate(2538) FIXME: Type 'boolean' cannot be used as an index type.
data.categoryLabel.newCount.bySubsetConfig[config.withSubset]
);
});
@@ -448,6 +453,7 @@ describe.each([
await createLabel(perTestCategoryName, labelName);
await assertLabelExists(perTestCategoryName, labelName);
await clickOn("undo");
// @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1.
await assertLabelDoesNotExist(perTestCategoryName);
await clickOn("redo");
await assertLabelExists(perTestCategoryName, labelName);
@@ -457,10 +463,12 @@ describe.each([
await setup(config);
await deleteLabel(perTestCategoryName, perTestLabelName);
// @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1.
await assertLabelDoesNotExist(perTestCategoryName);
await clickOn("undo");
await assertLabelExists(perTestCategoryName, perTestLabelName);
await clickOn("redo");
// @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1.
await assertLabelDoesNotExist(perTestCategoryName);
});
@@ -523,9 +531,10 @@ describe.each([
expect(result).toMatchSnapshot();
});
async function assertCategoryExists(categoryName) {
async function assertCategoryExists(categoryName: any) {
const handle = await waitByID(`${categoryName}:category-label`);
// @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
const result = await handle.evaluate((node) =>
node.getAttribute("aria-label")
);
@@ -533,7 +542,7 @@ describe.each([
return expect(result).toBe(categoryName);
}
async function assertLabelExists(categoryName, labelName) {
async function assertLabelExists(categoryName: any, labelName: any) {
await expect(page).toMatchElement(
getTestId(`${categoryName}:category-expand`)
);
@@ -545,11 +554,12 @@ describe.each([
);
expect(
// @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
await previous.evaluate((node) => node.getAttribute("aria-label"))
).toBe(labelName);
}
async function assertLabelDoesNotExist(categoryName, labelName) {
async function assertLabelDoesNotExist(categoryName: any, labelName: any) {
await expandCategory(categoryName);
const result = await page.$(
`[data-testid='categorical-value-${categoryName}-${labelName}']`
client/__tests__/e2e/e2eJestConfig.json
+4 -4
View File
@@ -1,10 +1,10 @@
{
"testRunner": "jest-circus/runner",
"preset": "jest-puppeteer",
"testMatch": ["**/__tests__/**/?(*.)(spec|test).js?(x)"],
"setupFiles": ["../setupMissingGlobals.js"],
"setupFilesAfterEnv": ["expect-puppeteer", "./puppeteer.setup.js"],
"globalSetup": "../globalSetup.js",
"testMatch": ["**/__tests__/**/?(*.)(spec|test).ts?(x)"],
"setupFiles": ["../setupMissingGlobals.ts"],
"setupFilesAfterEnv": ["expect-puppeteer", "./puppeteer.setup.ts"],
"globalSetup": "../globalSetup.ts",
"globalTeardown": "jest-environment-puppeteer/teardown",
"testEnvironment": "./screenshot_env.js"
}
client/__tests__/e2e/puppeteer.setup.js → client/__tests__/e2e/puppeteer.setup.ts
+2 -1
View File
@@ -23,6 +23,7 @@ beforeEach(async () => {
const userAgent = await browser.userAgent();
await page.setUserAgent(`${userAgent}bot`);
// @ts-expect-error ts-migrate(2341) FIXME: Property '_client' is private and only accessible ... Remove this comment to see the full error message
await page._client.send("Animation.setPlaybackRate", { playbackRate: 12 });
page.on("pageerror", (err) => {
@@ -49,7 +50,7 @@ beforeEach(async () => {
}
const errorMsgText = await Promise.all(
// TODO can we do this without internal properties?
msg.args().map((arg) => arg._remoteObject.description)
msg.args().map((arg: any) => arg._remoteObject.description)
);
throw new Error(`Console error: ${errorMsgText}`);
}
client/__tests__/e2e/puppeteerUtils.js → client/__tests__/e2e/puppeteerUtils.ts
+20 -17
View File
@@ -1,31 +1,31 @@
/* eslint-disable no-await-in-loop -- await in loop is needed to emulate sequential user actions */
export function getTestId(id) {
export function getTestId(id: any) {
return `[data-testid='${id}']`;
}
export function getTestClass(className) {
export function getTestClass(className: any) {
return `[data-testclass='${className}']`;
}
export async function waitByID(testId, props = {}) {
export async function waitByID(testId: any, props = {}) {
return page.waitForSelector(getTestId(testId), props);
}
export async function waitByClass(testClass, props = {}) {
export async function waitByClass(testClass: any, props = {}) {
return page.waitForSelector(`[data-testclass='${testClass}']`, props);
}
export async function waitForAllByIds(testIds) {
export async function waitForAllByIds(testIds: any) {
await Promise.all(
testIds.map((testId) => page.waitForSelector(getTestId(testId)))
testIds.map((testId: any) => page.waitForSelector(getTestId(testId)))
);
}
export async function getAllByClass(testClass) {
export async function getAllByClass(testClass: any) {
return page.$$(`[data-testclass=${testClass}]`);
}
export async function typeInto(testId, text) {
export async function typeInto(testId: any, text: any) {
// blueprint's typeahead is treating typing weird, clicking & waiting first solves this
// only works for text without special characters
await waitByID(testId);
@@ -36,7 +36,7 @@ export async function typeInto(testId, text) {
await page.type(selector, text);
}
export async function clearInputAndTypeInto(testId, text) {
export async function clearInputAndTypeInto(testId: any, text: any) {
await waitByID(testId);
const selector = getTestId(testId);
// only works for text without special characters
@@ -49,7 +49,7 @@ export async function clearInputAndTypeInto(testId, text) {
await page.type(selector, text);
}
export async function clickOn(testId, options = {}) {
export async function clickOn(testId: any, options = {}) {
await expect(page).toClick(getTestId(testId), options);
}
@@ -57,7 +57,7 @@ export async function clickOn(testId, options = {}) {
* (thuang): There are times when Puppeteer clicks on a button and the page doesn't respond.
* So I added clickOnUntil() to retry clicking until a given condition is met.
*/
export async function clickOnUntil(testId, assert) {
export async function clickOnUntil(testId: any, assert: any) {
const MAX_RETRY = 10;
const WAIT_FOR_MS = 200;
@@ -81,19 +81,19 @@ export async function clickOnUntil(testId, assert) {
}
}
export async function getOneElementInnerHTML(selector, options = {}) {
export async function getOneElementInnerHTML(selector: any, options = {}) {
await page.waitForSelector(selector, options);
return page.$eval(selector, (el) => el.innerHTML);
}
export async function getOneElementInnerText(selector) {
export async function getOneElementInnerText(selector: any) {
expect(page).toMatchElement(selector);
return page.$eval(selector, (el) => el.innerText);
return page.$eval(selector, (el) => (el as any).innerText);
}
export async function getElementCoordinates(testId) {
export async function getElementCoordinates(testId: any) {
return page.$eval(getTestId(testId), (elem) => {
const { left, top } = elem.getBoundingClientRect();
return [left, top];
@@ -101,12 +101,14 @@ export async function getElementCoordinates(testId) {
}
async function clickTermsOfService() {
// @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1.
if (!(await isElementPresent(getTestId("tos-cookies-accept")))) return;
await clickOn("tos-cookies-accept");
}
async function nameNewAnnotation() {
// @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1.
if (await isElementPresent(getTestId("annotation-dialog"))) {
await typeInto("new-annotation-name", "ignoreE2E");
await clickOn("submit-annotation");
@@ -116,7 +118,7 @@ async function nameNewAnnotation() {
}
}
export async function goToPage(url) {
export async function goToPage(url: any) {
await page.goto(url, {
waitUntil: "networkidle0",
});
@@ -125,7 +127,8 @@ export async function goToPage(url) {
await clickTermsOfService();
}
export async function isElementPresent(selector, options) {
export async function isElementPresent(selector: any, options: any) {
// @ts-expect-error ts-migrate(2554) FIXME: Expected 1 arguments, but got 2.
return Boolean(await page.$(selector, options));
}
/* eslint-enable no-await-in-loop -- await in loop is needed to emulate sequential user actions */
client/__tests__/e2e/screenshot_env.js
+1
View File
@@ -2,6 +2,7 @@ const PuppeteerEnvironment = require("jest-environment-puppeteer");
require("jest-circus");
const ENV_DEFAULT = require("../../../environment.default.json");
// @ts-expect-error ts-migrate(2451) FIXME: Cannot redeclare block-scoped variable 'takeScreen... Remove this comment to see the full error message
const takeScreenshot = require("./takeScreenshot");
class ScreenshotEnvironment extends PuppeteerEnvironment {
client/__tests__/globalSetup.js → client/__tests__/globalSetup.ts
+1
View File
@@ -1,3 +1,4 @@
// @ts-ignore FIXME revisit from ts-migrate
const {
SecretsManagerClient,
GetSecretValueCommand,
client/__tests__/reducers/cascade.test.js → client/__tests__/reducers/cascade.test.ts
+12 -2
View File
@@ -20,7 +20,12 @@ describe("cascade", () => {
const reducer = cascadeReducers([
[
"foo",
(currentState, action, nextSharedState, prevSharedState) => {
(
currentState: any,
action: any,
nextSharedState: any,
prevSharedState: any
) => {
expect(currentState).toBeUndefined();
expect(action).toEqual(topLevelAction);
expect(nextSharedState).toStrictEqual({});
@@ -30,7 +35,12 @@ describe("cascade", () => {
],
[
"bar",
(currentState, action, nextSharedState, prevSharedState) => {
(
currentState: any,
action: any,
nextSharedState: any,
prevSharedState: any
) => {
expect(currentState).toBeUndefined();
expect(action).toEqual(topLevelAction);
expect(nextSharedState).toStrictEqual({ foo: 0 });
client/__tests__/reducers/genesets.test.js → client/__tests__/reducers/genesets.test.ts
+2
View File
@@ -501,6 +501,7 @@ describe("geneset: set tid", () => {
test("not a number error", () => {
expect(() => {
genesetsReducer(
// @ts-expect-error ts-migrate(2322) FIXME: Type 'number' is not assignable to type 'undefined... Remove this comment to see the full error message
{ lastTid: 1 },
{
type: "geneset: set tid",
@@ -513,6 +514,7 @@ describe("geneset: set tid", () => {
test("decrement error", () => {
expect(() => {
genesetsReducer(
// @ts-expect-error ts-migrate(2322) FIXME: Type 'number' is not assignable to type 'undefined... Remove this comment to see the full error message
{ lastTid: 1 },
{
type: "geneset: set tid",
client/__tests__/reducers/genesetsUI.test.js → client/__tests__/reducers/genesetsUI.test.ts
View File
client/__tests__/reducers/undoable.test.js → client/__tests__/reducers/undoable.test.ts
+4 -3
View File
@@ -2,6 +2,7 @@ import undoable from "../../src/reducers/undoable";
describe("create", () => {
test("no keys", () => {
// @ts-expect-error ts-migrate(2554) FIXME: Expected 2-3 arguments, but got 1.
expect(() => undoable(() => {})).toThrow();
expect(() => undoable(() => {}, null)).toThrow();
expect(() => undoable(() => {}, [])).toThrow();
@@ -23,7 +24,7 @@ describe("create", () => {
describe("undo", () => {
test("expected state modifications", () => {
const initialState = { a: 0, b: 1000 };
const reducer = (state) => {
const reducer = (state: any) => {
return { a: state.a + 1, b: state.b + 1 };
};
const undoableReducer = undoable(reducer, ["a"]);
@@ -43,10 +44,10 @@ describe("undo", () => {
describe("redo", () => {
const initialState = { a: 0, b: 1000 };
const reducer = (state) => {
const reducer = (state: any) => {
return { a: state.a + 1, b: state.b + 1 };
};
let UR;
let UR: any;
beforeEach(() => {
UR = undoable(reducer, ["a"]);
client/__tests__/setupMissingGlobals.js → client/__tests__/setupMissingGlobals.ts
+1
View File
@@ -5,5 +5,6 @@ the jest test environment).
import { TextDecoder, TextEncoder } from "util";
// @ts-expect-error ts-migrate(2322) FIXME: Type 'typeof TextDecoder' is not assignable to typ... Remove this comment to see the full error message
global.TextDecoder = TextDecoder;
global.TextEncoder = TextEncoder;
client/__tests__/util/actionHelpers.test.js → client/__tests__/util/actionHelpers.test.ts
View File
client/__tests__/util/annoMatrix/annoMatrix.test.js → client/__tests__/util/annoMatrix/annoMatrix.test.ts
+22 -17
View File
@@ -14,10 +14,11 @@ import { Dataframe } from "../../../src/util/dataframe";
enableFetchMocks();
describe("AnnoMatrix", () => {
let annoMatrix;
let annoMatrix: any;
beforeEach(async () => {
fetch.resetMocks(); // reset all fetch mocking state
(fetch as any).resetMocks(); // reset all fetch mocking state
// reset all fetch mocking state
annoMatrix = new AnnoMatrixLoader(
serverMocks.baseDataURL,
serverMocks.schema.schema
@@ -36,7 +37,7 @@ describe("AnnoMatrix", () => {
});
test("simple single column fetch", async () => {
fetch.once(serverMocks.annotationsObs(["name_0"]));
(fetch as any).once(serverMocks.annotationsObs(["name_0"]));
const df = await annoMatrix.fetch("obs", "name_0");
expect(df).toBeInstanceOf(Dataframe);
@@ -45,7 +46,7 @@ describe("AnnoMatrix", () => {
});
test("simple multi column fetch", async () => {
fetch
(fetch as any)
.once(serverMocks.annotationsObs(["name_0"]))
.once(serverMocks.annotationsObs(["n_genes"]));
@@ -55,9 +56,11 @@ describe("AnnoMatrix", () => {
});
describe("fetch from field", () => {
const getLastTwo = async (field) => {
const getLastTwo = async (field: any) => {
const columnNames = annoMatrix.getMatrixColumns(field).slice(-2);
fetch.mockResponses(...columnNames.map(() => serverMocks.responder));
(fetch as any).mockResponses(
...columnNames.map(() => serverMocks.responder)
);
await expect(
annoMatrix.fetch(field, columnNames)
).resolves.toBeInstanceOf(Dataframe);
@@ -70,19 +73,19 @@ describe("AnnoMatrix", () => {
test("fetch - test all query forms", async () => {
// single string is a column name
fetch.once(serverMocks.annotationsObs(["n_genes"]));
(fetch as any).once(serverMocks.annotationsObs(["n_genes"]));
await expect(annoMatrix.fetch("obs", "n_genes")).resolves.toBeInstanceOf(
Dataframe
);
// array of column names, expecting n_genes to be cached.
fetch.once(serverMocks.annotationsObs(["percent_mito"]));
(fetch as any).once(serverMocks.annotationsObs(["percent_mito"]));
await expect(
annoMatrix.fetch("obs", ["n_genes", "percent_mito"])
).resolves.toBeInstanceOf(Dataframe);
// more complex value filter query, enumerated
fetch.once(serverMocks.responder);
(fetch as any).once(serverMocks.responder);
await expect(
annoMatrix.fetch("X", {
where: {
@@ -95,7 +98,7 @@ describe("AnnoMatrix", () => {
// more complex value filter query, range
const varIndex = annoMatrix.schema.annotations.var.index;
fetch
(fetch as any)
.once(
serverMocks.withExpected("/data/var", [[`var:${varIndex}`, "SUMO3"]])
)
@@ -171,7 +174,7 @@ describe("AnnoMatrix", () => {
expect(am1.nObs).toEqual(am2.nObs);
expect(am1.nVar).toEqual(am2.nVar);
fetch
(fetch as any)
.once(serverMocks.annotationsObs(["n_genes"]))
.once(serverMocks.annotationsObs(["n_genes"]));
const ng1 = await am1.fetch("obs", "n_genes");
@@ -185,9 +188,10 @@ describe("AnnoMatrix", () => {
});
describe("add/drop column", () => {
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'base' implicitly has an 'any' type.
async function addDrop(base) {
expect(base.getMatrixColumns("obs")).not.toContain("foo");
fetch.mockRejectOnce(new Error("unknown column name"));
(fetch as any).mockRejectOnce(new Error("unknown column name"));
await expect(base.fetch("obs", "foo")).rejects.toThrow(
"unknown column name"
);
@@ -212,7 +216,7 @@ describe("AnnoMatrix", () => {
const am2 = am1.dropObsColumn("foo");
expect(base.getMatrixColumns("obs")).not.toContain("foo");
expect(am2.getMatrixColumns("obs")).not.toContain("foo");
fetch.mockRejectOnce(new Error("unknown column name"));
(fetch as any).mockRejectOnce(new Error("unknown column name"));
await expect(am2.fetch("obs", "foo")).rejects.toThrow(
"unknown column name"
);
@@ -235,14 +239,14 @@ describe("AnnoMatrix", () => {
const am4 = clip(am3, 0, 1);
await addDrop(am4);
fetch.mockResponse(serverMocks.responder);
(fetch as any).mockResponse(serverMocks.responder);
await am1.fetch("obs", am1.getMatrixColumns("obs"));
await am2.fetch("obs", am2.getMatrixColumns("obs"));
await am3.fetch("obs", am3.getMatrixColumns("obs"));
await am4.fetch("obs", am4.getMatrixColumns("obs"));
fetch.resetMocks();
(fetch as any).resetMocks();
await addDrop(am1);
await addDrop(am2);
@@ -252,6 +256,7 @@ describe("AnnoMatrix", () => {
});
describe("setObsColumnValues", () => {
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'base' implicitly has an 'any' type.
async function addSetDrop(base) {
/* add column */
let am = base.addObsColumn(
@@ -287,7 +292,7 @@ describe("AnnoMatrix", () => {
);
/* drop column */
fetch.mockRejectOnce(new Error("unknown column name"));
(fetch as any).mockRejectOnce(new Error("unknown column name"));
am = am1.dropObsColumn("test");
await expect(am.fetch("obs", "test")).rejects.toThrow(
"unknown column name"
@@ -308,7 +313,7 @@ describe("AnnoMatrix", () => {
const am3 = isubset(annoMatrix, [10, 1, 0, 30, 2]);
await addSetDrop(am3);
fetch.mockResponse(serverMocks.responder);
(fetch as any).mockResponse(serverMocks.responder);
await am1.fetch("obs", am1.getMatrixColumns("obs"));
await am2.fetch("obs", am2.getMatrixColumns("obs"));
client/__tests__/util/annoMatrix/crossfilter.test.js → client/__tests__/util/annoMatrix/crossfilter.test.ts
+60 -36
View File
@@ -17,11 +17,12 @@ import { rangeFill } from "../../../src/util/range";
enableFetchMocks();
describe("AnnoMatrixCrossfilter", () => {
let annoMatrix;
let crossfilter;
let annoMatrix: any;
let crossfilter: any;
beforeEach(async () => {
fetch.resetMocks(); // reset all fetch mocking state
(fetch as any).resetMocks(); // reset all fetch mocking state
// reset all fetch mocking state
annoMatrix = new AnnoMatrixLoader(
serverMocks.baseDataURL,
serverMocks.schema.schema
@@ -67,7 +68,9 @@ describe("AnnoMatrixCrossfilter", () => {
crossfilter.obsCrossfilter.hasDimension("obs/louvain")
).toBeFalsy();
fetch.once(serverMocks.dataframeResponse(["louvain"], [obsLouvain]));
(fetch as any).once(
serverMocks.dataframeResponse(["louvain"], [obsLouvain])
);
let newCrossfilter = await crossfilter.select("obs", "louvain", {
mode: "none",
});
@@ -76,7 +79,7 @@ describe("AnnoMatrixCrossfilter", () => {
expect(
newCrossfilter.obsCrossfilter.hasDimension("obs/louvain")
).toBeTruthy();
expect(fetch.mock.calls).toHaveLength(1);
expect((fetch as any).mock.calls).toHaveLength(1);
newCrossfilter = await crossfilter.select("obs", "louvain", {
mode: "all",
@@ -87,7 +90,9 @@ describe("AnnoMatrixCrossfilter", () => {
test("simple column select", async () => {
let xfltr;
fetch.once(serverMocks.dataframeResponse(["louvain"], [obsLouvain]));
(fetch as any).once(
serverMocks.dataframeResponse(["louvain"], [obsLouvain])
);
xfltr = await crossfilter.select("obs", "louvain", {
mode: "exact",
values: ["NK cells", "B cells"],
@@ -105,6 +110,7 @@ describe("AnnoMatrixCrossfilter", () => {
expect(xfltr.allSelectedLabels()).toEqual(
Int32Array.from(
obsLouvain.reduce((acc, val, idx) => {
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'number' is not assignable to par... Remove this comment to see the full error message
if (val === "NK cells" || val === "B cells") acc.push(idx);
return acc;
}, [])
@@ -124,10 +130,11 @@ describe("AnnoMatrixCrossfilter", () => {
const values = df.col("louvain").asArray();
const selected = xfltr.allSelectedMask();
values.every(
(val, idx) => !["NK cells", "B cells"].includes(val) !== !selected[idx]
(val: any, idx: any) =>
!["NK cells", "B cells"].includes(val) !== !selected[idx]
);
fetch.once(
(fetch as any).once(
serverMocks.dataframeResponse(["n_genes"], [new Int32Array(obsNGenes)])
);
xfltr = await xfltr.select("obs", "n_genes", {
@@ -146,6 +153,7 @@ describe("AnnoMatrixCrossfilter", () => {
val < 500 &&
(louvain === "NK cells" || louvain === "B cells")
)
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'number' is not assignable to par... Remove this comment to see the full error message
acc.push(idx);
return acc;
}, [])
@@ -160,7 +168,7 @@ describe("AnnoMatrixCrossfilter", () => {
const varIndex = annoMatrix.schema.annotations.var.index;
const { nObs } = annoMatrix.schema.dataframe;
fetch.once(
(fetch as any).once(
serverMocks.dataframeResponse(
["TEST"],
[rangeFill(new Float32Array(nObs), 0, 0.1)]
@@ -196,14 +204,16 @@ describe("AnnoMatrixCrossfilter", () => {
});
const values = df.icol(0).asArray();
const selected = xfltr.allSelectedMask();
values.every((val, idx) => !(val >= 0 && val <= 50) !== !selected[idx]);
expect(selected.reduce((acc, val) => (val ? acc + 1 : acc), 0)).toEqual(
xfltr.countSelected()
values.every(
(val: any, idx: any) => !(val >= 0 && val <= 50) !== !selected[idx]
);
expect(
selected.reduce((acc: any, val: any) => (val ? acc + 1 : acc), 0)
).toEqual(xfltr.countSelected());
});
test("spatial column select", async () => {
fetch.once(
(fetch as any).once(
serverMocks.dataframeResponse(
["umap_0", "umap_1"],
[Float32Array.from(embUmap[0]), Float32Array.from(embUmap[1])]
@@ -222,6 +232,7 @@ describe("AnnoMatrixCrossfilter", () => {
test("select on subset", async () => {
const mask = new Uint8Array(annoMatrix.nObs).fill(0);
for (let i = 0; i < mask.length; i += 2) {
// @ts-expect-error ts-migrate(2322) FIXME: Type 'boolean' is not assignable to type 'number'.
mask[i] = true;
}
const annoMatrixSubset = isubsetMask(annoMatrix, mask);
@@ -230,7 +241,9 @@ describe("AnnoMatrixCrossfilter", () => {
let xfltr = new AnnoMatrixObsCrossfilter(annoMatrixSubset);
expect(xfltr.countSelected()).toEqual(annoMatrixSubset.nObs);
fetch.once(serverMocks.dataframeResponse(["louvain"], [obsLouvain]));
(fetch as any).once(
serverMocks.dataframeResponse(["louvain"], [obsLouvain])
);
xfltr = await xfltr.select("obs", "louvain", {
mode: "exact",
values: ["NK cells", "B cells"],
@@ -243,7 +256,8 @@ describe("AnnoMatrixCrossfilter", () => {
const values = df.col("louvain").asArray();
const selected = xfltr.allSelectedMask();
values.every(
(val, idx) => !["NK cells", "B cells"].includes(val) !== !selected[idx]
(val: any, idx: any) =>
!["NK cells", "B cells"].includes(val) !== !selected[idx]
);
});
@@ -256,7 +270,7 @@ describe("AnnoMatrixCrossfilter", () => {
"unable to obsSelect upon the var dimension"
);
fetch.mockRejectOnce(new Error("unknown column name"));
(fetch as any).mockRejectOnce(new Error("unknown column name"));
await expect(crossfilter.select("obs", "foo")).rejects.toThrow(
"unknown column name"
);
@@ -267,24 +281,27 @@ describe("AnnoMatrixCrossfilter", () => {
/*
test the matrix mutators via crossfilter proxy
*/
async function helperAddTestCol(cf, colName, colSchema = null) {
async function helperAddTestCol(cf: any, colName: any, colSchema = null) {
expect(
cf.annoMatrix.getMatrixColumns("obs").includes(colName)
).toBeFalsy();
if (colSchema === null) {
// @ts-expect-error ts-migrate(2322) FIXME: Type '{ name: any; type: string; categories: strin... Remove this comment to see the full error message
colSchema = {
name: colName,
type: "categorical",
categories: ["toasty"],
};
}
// @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
colSchema.name = colName;
// @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
const initValue = colSchema.categories[0];
const xfltr = cf.addObsColumn(colSchema, Array, initValue);
expect(
xfltr.annoMatrix.schema.annotations.obs.columns.filter(
(v) => v.name === colName
(v: any) => v.name === colName
)
).toHaveLength(1);
const df = await xfltr.annoMatrix.fetch("obs", colName);
@@ -314,7 +331,7 @@ describe("AnnoMatrixCrossfilter", () => {
});
expect(
xfltr.annoMatrix.schema.annotations.obs.columns.filter(
(v) => v.name === "foo"
(v: any) => v.name === "foo"
)
).toHaveLength(1);
@@ -324,7 +341,7 @@ describe("AnnoMatrixCrossfilter", () => {
df
.col("foo")
.asArray()
.every((v) => v === "A")
.every((v: any) => v === "A")
).toBeTruthy();
// check that we catch dups
@@ -361,11 +378,11 @@ describe("AnnoMatrixCrossfilter", () => {
xfltr = xfltr.dropObsColumn("foo");
expect(
xfltr.annoMatrix.schema.annotations.obs.columns.filter(
(v) => v.name === "foo"
(v: any) => v.name === "foo"
)
).toHaveLength(0);
expect(xfltr.annoMatrix.schema.annotations.obsByName.foo).toBeUndefined();
fetch.mockRejectOnce(new Error("unknown column name"));
(fetch as any).mockRejectOnce(new Error("unknown column name"));
await expect(xfltr.annoMatrix.fetch("obs", "foo")).rejects.toThrow(
"unknown column name"
);
@@ -378,7 +395,7 @@ describe("AnnoMatrixCrossfilter", () => {
});
xfltr = xfltr.dropObsColumn("bar");
fetch.mockRejectOnce(new Error("unknown column name"));
(fetch as any).mockRejectOnce(new Error("unknown column name"));
await expect(xfltr.select("obs", "bar", { mode: "all" })).rejects.toThrow(
"unknown column name"
);
@@ -404,7 +421,7 @@ describe("AnnoMatrixCrossfilter", () => {
type: "categorical",
});
fetch.mockRejectOnce(new Error("unknown column name"));
(fetch as any).mockRejectOnce(new Error("unknown column name"));
await expect(xfltr.annoMatrix.fetch("obs", "foo")).rejects.toThrow(
"unknown column name"
);
@@ -419,7 +436,7 @@ describe("AnnoMatrixCrossfilter", () => {
});
xfltr = xfltr.renameObsColumn("bar", "xyz");
fetch.mockRejectOnce(new Error("unknown column name"));
(fetch as any).mockRejectOnce(new Error("unknown column name"));
await expect(xfltr.select("obs", "bar", { mode: "all" })).rejects.toThrow(
"unknown column name"
);
@@ -429,7 +446,7 @@ describe("AnnoMatrixCrossfilter", () => {
});
test("addObsAnnoCategory", async () => {
let xfltr;
let xfltr: any;
// catch unknown or readonly columns
expect(() => crossfilter.addObsAnnoCategory("louvain", "mumble")).toThrow(
@@ -440,6 +457,7 @@ describe("AnnoMatrixCrossfilter", () => {
).toThrow("Unknown or readonly obs column");
// add a column and then add category to it
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type '{ name: string; type: string; ca... Remove this comment to see the full error message
xfltr = await helperAddTestCol(crossfilter, "foo", {
name: "foo",
type: "categorical",
@@ -458,6 +476,7 @@ describe("AnnoMatrixCrossfilter", () => {
);
// now same, but ensure we have built an index before doing the operation
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type '{ name: string; type: string; ca... Remove this comment to see the full error message
xfltr = await helperAddTestCol(crossfilter, "bar", {
name: "bar",
type: "categorical",
@@ -486,6 +505,7 @@ describe("AnnoMatrixCrossfilter", () => {
crossfilter.removeObsAnnoCategory("undefined-name", "mumble")
).rejects.toThrow("Unknown or readonly obs column");
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type '{ name: string; type: string; ca... Remove this comment to see the full error message
xfltr = await helperAddTestCol(crossfilter, "foo", {
name: "foo",
type: "categorical",
@@ -496,7 +516,7 @@ describe("AnnoMatrixCrossfilter", () => {
(await xfltr.annoMatrix.fetch("obs", "foo"))
.col("foo")
.asArray()
.every((v) => v === "unassigned")
.every((v: any) => v === "unassigned")
).toBeTruthy();
expect(xfltr.annoMatrix.getColumnSchema("obs", "foo")).toMatchObject({
name: "foo",
@@ -515,7 +535,7 @@ describe("AnnoMatrixCrossfilter", () => {
(await xfltr1.annoMatrix.fetch("obs", "foo"))
.col("foo")
.asArray()
.every((v) => v === "unassigned")
.every((v: any) => v === "unassigned")
).toBeTruthy();
expect(xfltr1.annoMatrix.getColumnSchema("obs", "foo")).toMatchObject({
name: "foo",
@@ -538,7 +558,7 @@ describe("AnnoMatrixCrossfilter", () => {
(await xfltr2.annoMatrix.fetch("obs", "foo"))
.col("foo")
.asArray()
.every((v) => v === "red")
.every((v: any) => v === "red")
).toBeTruthy();
expect(xfltr2.annoMatrix.getColumnSchema("obs", "foo")).toMatchObject({
name: "foo",
@@ -556,6 +576,7 @@ describe("AnnoMatrixCrossfilter", () => {
crossfilter.setObsColumnValues("undefined-name", [0], "mumble")
).rejects.toThrow("Unknown or readonly obs column");
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type '{ name: string; type: string; ca... Remove this comment to see the full error message
let xfltr = await helperAddTestCol(crossfilter, "foo", {
name: "foo",
type: "categorical",
@@ -573,7 +594,7 @@ describe("AnnoMatrixCrossfilter", () => {
(await xfltr.annoMatrix.fetch("obs", "foo"))
.col("foo")
.asArray()
.every((v) => v === "unassigned")
.every((v: any) => v === "unassigned")
).toBeTruthy();
const xfltr1 = await xfltr.setObsColumnValues("foo", [0, 10], "purple");
expect(
@@ -581,7 +602,7 @@ describe("AnnoMatrixCrossfilter", () => {
.col("foo")
.asArray()
.every(
(v, i) =>
(v: any, i: any) =>
v === "unassigned" || (v === "purple" && (i === 0 || i === 10))
)
).toBeTruthy();
@@ -615,6 +636,7 @@ describe("AnnoMatrixCrossfilter", () => {
crossfilter.resetObsColumnValues("undefined-name", "red", "blue")
).rejects.toThrow("Unknown or readonly obs column");
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type '{ name: string; type: string; ca... Remove this comment to see the full error message
let xfltr = await helperAddTestCol(crossfilter, "foo", {
name: "foo",
type: "categorical",
@@ -639,7 +661,7 @@ describe("AnnoMatrixCrossfilter", () => {
(await xfltr1.annoMatrix.fetch("obs", "foo"))
.col("foo")
.asArray()
.filter((v) => v === "purple")
.filter((v: any) => v === "purple")
).toHaveLength(2);
xfltr1 = await xfltr1.resetObsColumnValues("foo", "purple", "magenta");
@@ -647,13 +669,13 @@ describe("AnnoMatrixCrossfilter", () => {
(await xfltr1.annoMatrix.fetch("obs", "foo"))
.col("foo")
.asArray()
.filter((v) => v === "magenta")
.filter((v: any) => v === "magenta")
).toHaveLength(2);
expect(
(await xfltr1.annoMatrix.fetch("obs", "foo"))
.col("foo")
.asArray()
.filter((v) => v === "purple")
.filter((v: any) => v === "purple")
).toHaveLength(0);
expect(xfltr1.annoMatrix.getColumnSchema("obs", "foo")).toMatchObject({
name: "foo",
@@ -673,12 +695,14 @@ describe("AnnoMatrixCrossfilter", () => {
describe("edge cases", () => {
test("transition from empty annoMatrix", async () => {
// select before fetch needs to work
fetch.once(serverMocks.dataframeResponse(["louvain"], [obsLouvain]));
(fetch as any).once(
serverMocks.dataframeResponse(["louvain"], [obsLouvain])
);
const xfltr = await crossfilter.select("obs", "louvain", {
mode: "exact",
values: "B cells",
});
expect(fetch.mock.calls).toHaveLength(1);
expect((fetch as any).mock.calls).toHaveLength(1);
expect(xfltr.obsCrossfilter.hasDimension("obs/louvain")).toBeTruthy();
expect(xfltr.obsCrossfilter.all()).toBe(xfltr.annoMatrix._cache.obs);
expect(xfltr.countSelected()).toEqual(
client/__tests__/util/annoMatrix/serverMocks/index.js → client/__tests__/util/annoMatrix/serverMocks/index.ts
+1 -1
View File
@@ -1,6 +1,6 @@
export const baseDataURL = "https://a.fake.url/api/v0.2";
window.CELLXGENE = {
(window as any).CELLXGENE = {
API: {
prefix: baseDataURL,
version: "v0.2/",
client/__tests__/util/annoMatrix/serverMocks/routes.js → client/__tests__/util/annoMatrix/serverMocks/routes.ts
+41 -22
View File
@@ -14,7 +14,7 @@ const indexedSchema = {
),
};
function makeMockColumn(s, length) {
function makeMockColumn(s: any, length: any) {
const { type } = s;
switch (type) {
case "int32":
@@ -37,20 +37,22 @@ function makeMockColumn(s, length) {
}
}
function getEncodedDataframe(colNames, length, colSchemas) {
function getEncodedDataframe(colNames: any, length: any, colSchemas: any) {
const colIndex = new KeyIndex(colNames);
const columns = colSchemas.map((s) => makeMockColumn(s, length));
const columns = colSchemas.map((s: any) => makeMockColumn(s, length));
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
const df = new Dataframe([length, colNames.length], columns, null, colIndex);
const body = encodeMatrixFBS(df);
return body;
}
export function dataframeResponse(colNames, columns) {
export function dataframeResponse(colNames: any, columns: any) {
const colIndex = new KeyIndex(colNames);
const df = new Dataframe(
[columns[0].length, colNames.length],
columns,
null,
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
colIndex
);
const body = encodeMatrixFBS(df);
@@ -60,15 +62,19 @@ export function dataframeResponse(colNames, columns) {
return () => Promise.resolve({ body, init: { status: 200, headers } });
}
function annotationObsResponse(request) {
function annotationObsResponse(request: any) {
const url = new URL(request.url);
const params = Array.from(url.searchParams.entries());
const params = Array.from((url.searchParams as any).entries());
const names = params
// @ts-expect-error ts-migrate(2769) FIXME: No overload matches this call.
.filter(([k]) => k === "annotation-name")
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type '([, v]: [any, any]) => any' is n... Remove this comment to see the full error message
.map(([, v]) => v);
// @ts-expect-error ts-migrate(2538) FIXME: Type 'unknown' cannot be used as an index type.
if (!names.every((n) => indexedSchema.obsByName[n])) {
return Promise.reject(new Error("bad obs annotation name in URL"));
}
// @ts-expect-error ts-migrate(2538) FIXME: Type 'unknown' cannot be used as an index type.
const colSchemas = names.map((n) => indexedSchema.obsByName[n]);
const body = getEncodedDataframe(
names,
@@ -85,15 +91,19 @@ function annotationObsResponse(request) {
});
}
function annotationVarResponse(request) {
function annotationVarResponse(request: any) {
const url = new URL(request.url);
const params = Array.from(url.searchParams.entries());
const params = Array.from((url.searchParams as any).entries());
const names = params
// @ts-expect-error ts-migrate(2769) FIXME: No overload matches this call.
.filter(([k]) => k === "annotation-name")
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type '([, v]: [any, any]) => any' is n... Remove this comment to see the full error message
.map(([, v]) => v);
// @ts-expect-error ts-migrate(2538) FIXME: Type 'unknown' cannot be used as an index type.
if (!names.every((n) => indexedSchema.varByName[n])) {
return Promise.reject(new Error("bad var annotation name in URL"));
}
// @ts-expect-error ts-migrate(2538) FIXME: Type 'unknown' cannot be used as an index type.
const colSchemas = names.map((n) => indexedSchema.varByName[n]);
const body = getEncodedDataframe(
names,
@@ -110,15 +120,19 @@ function annotationVarResponse(request) {
});
}
function layoutObsResponse(request) {
function layoutObsResponse(request: any) {
const url = new URL(request.url);
const params = Array.from(url.searchParams.entries());
const params = Array.from((url.searchParams as any).entries());
// @ts-expect-error ts-migrate(2769) FIXME: No overload matches this call.
const names = params.filter(([k]) => k === "layout-name").map(([, v]) => v);
// @ts-expect-error ts-migrate(2538) FIXME: Type 'unknown' cannot be used as an index type.
if (!names.every((n) => indexedSchema.embByName[n])) {
return Promise.reject(new Error("bad layout name in URL"));
}
// @ts-expect-error ts-migrate(2538) FIXME: Type 'unknown' cannot be used as an index type.
const dims = names.map((n) => indexedSchema.embByName[n].dims).flat();
const colSchemas = names
// @ts-expect-error ts-migrate(2538) FIXME: Type 'unknown' cannot be used as an index type.
.map((n) => [indexedSchema.embByName[n], indexedSchema.embByName[n]])
.flat();
const body = getEncodedDataframe(
@@ -136,11 +150,11 @@ function layoutObsResponse(request) {
});
}
function dataVarResponse(request) {
function dataVarResponse(request: any) {
const url = new URL(request.url);
const params = Array.from(url.searchParams.entries());
const params = Array.from((url.searchParams as any).entries());
const colNames = params.map((v) => `${v[0]}/${v[1]}`);
const colNames = params.map((v) => `${(v as any)[0]}/${(v as any)[1]}`);
const colSchemas = colNames.map(() => schema.schema.dataframe);
const body = getEncodedDataframe(
colNames,
@@ -157,7 +171,7 @@ function dataVarResponse(request) {
});
}
export function responder(request) {
export function responder(request: any) {
const url = new URL(request.url);
const { pathname } = url;
if (pathname.endsWith("/annotations/obs")) {
@@ -175,25 +189,30 @@ export function responder(request) {
return Promise.reject(new Error("bad URL"));
}
export function withExpected(expectedURL, expectedParams) {
export function withExpected(expectedURL: any, expectedParams: any) {
/*
Do some additional error checking
*/
return (request) => {
return (request: any) => {
// if URL is bogus, reject the promise
const url = new URL(request.url);
if (!url.pathname.endsWith(expectedURL)) {
return Promise.reject(new Error("Unexpected URL!"));
}
const params = Array.from(url.searchParams.entries()).sort(
(a, b) => a[0] < b[0]
const params = Array.from((url.searchParams as any).entries()).sort(
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type '(a: unknown, b: unknown) => bool... Remove this comment to see the full error message
(a, b) => (a as any)[0] < (b as any)[0]
);
expectedParams = expectedParams.slice().sort((a, b) => a[0] < b[0]);
expectedParams = expectedParams
.slice()
.sort((a: any, b: any) => a[0] < b[0]);
if (
params.length !== expectedParams.length ||
!params.every(
(p, i) => p[0] === expectedParams[i][0] && p[1] === expectedParams[i][1]
(p, i) =>
(p as any)[0] === expectedParams[i][0] &&
(p as any)[1] === expectedParams[i][1]
)
) {
return Promise.reject(new Error("unexpected name requested in URL"));
@@ -203,9 +222,9 @@ export function withExpected(expectedURL, expectedParams) {
};
}
export function annotationsObs(names) {
export function annotationsObs(names: any) {
return withExpected(
"/annotations/obs",
names.map((name) => ["annotation-name", name])
names.map((name: any) => ["annotation-name", name])
);
}
client/__tests__/util/annoMatrix/serverMocks/schema.js → client/__tests__/util/annoMatrix/serverMocks/schema.ts
View File
client/__tests__/util/annoMatrix/whereCache.test.js → client/__tests__/util/annoMatrix/whereCache.test.ts
+8 -3
View File
@@ -218,10 +218,15 @@ describe("whereCache", () => {
},
})
);
expect(wc.where.field.queryField.has("queryColumn")).toEqual(true);
expect(wc.where.field.queryField.get("queryColumn")).toBeInstanceOf(Map);
// @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
expect((wc.where as any).field.queryField.has("queryColumn")).toEqual(true);
expect(
wc.where.field.queryField.get("queryColumn").has("queryValue")
// @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
(wc.where as any).field.queryField.get("queryColumn")
).toBeInstanceOf(Map);
expect(
// @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
(wc.where as any).field.queryField.get("queryColumn").has("queryValue")
).toEqual(true);
expect(_whereCacheGet(wc, schema, "field", query)).toEqual([0, 1, 2]);
});
client/__tests__/util/centroid.test.js → client/__tests__/util/centroid.test.ts
+5 -5
View File
@@ -8,9 +8,9 @@ import { indexEntireSchema } from "../../src/util/stateManager/schemaHelpers";
import { _normalizeCategoricalSchema } from "../../src/annoMatrix/schema";
describe("centroid", () => {
let schema;
let obsAnnotations;
let obsLayout;
let schema: any;
let obsAnnotations: any;
let obsLayout: any;
beforeAll(() => {
schema = indexEntireSchema(cloneDeep(REST.schema.schema));
@@ -44,7 +44,7 @@ describe("centroid", () => {
quantile([0.5], obsLayout.col("umap_1").asArray())[0],
];
centroidResult.forEach((coordinate) => {
centroidResult.forEach((coordinate: any) => {
expect(coordinate).toEqual(expectedResult);
});
});
@@ -68,7 +68,7 @@ describe("centroid", () => {
quantile([0.5], obsLayout.col("umap_1").asArray())[0],
];
centroidResult.forEach((coordinate) => {
centroidResult.forEach((coordinate: any) => {
expect(coordinate).toEqual(expectedResult);
});
});
client/__tests__/util/dataframe/dataframe.test.js → client/__tests__/util/dataframe/dataframe.test.ts
+40 -2
View File
@@ -29,6 +29,7 @@ describe("dataframe constructor", () => {
const df = new Dataframe.Dataframe(
[3, 2],
[new Int32Array([0, 1, 2]), new Int32Array([3, 4, 5])],
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'DenseInt32Index' is not assignab... Remove this comment to see the full error message
new Dataframe.DenseInt32Index([2, 1, 0]),
new Dataframe.KeyIndex(["A", "B"])
);
@@ -55,6 +56,7 @@ describe("simple data access", () => {
new Float64Array([0.0, Number.NaN, Number.POSITIVE_INFINITY, 3.14159]),
["red", "blue", "green", "nan"],
],
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'DenseInt32Index' is not assignab... Remove this comment to see the full error message
new Dataframe.DenseInt32Index([3, 2, 1, 0]),
new Dataframe.KeyIndex(["numbers", "colors"])
);
@@ -139,10 +141,12 @@ describe("dataframe subsetting", () => {
["red", "green", "blue"],
],
null, // identity index
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
new Dataframe.KeyIndex(["int32", "string", "float32", "colors"])
);
test("all rows, one column", () => {
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'string[]' is not assignable to p... Remove this comment to see the full error message
const dfA = sourceDf.subset(null, ["colors"]);
expect(dfA).toBeDefined();
expect(dfA.dims).toEqual([3, 1]);
@@ -158,6 +162,7 @@ describe("dataframe subsetting", () => {
});
test("all rows, two columns", () => {
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'string[]' is not assignable to p... Remove this comment to see the full error message
const dfB = sourceDf.subset(null, ["float32", "colors"]);
expect(dfB).toBeDefined();
expect(dfB.dims).toEqual([3, 2]);
@@ -227,6 +232,7 @@ describe("dataframe subsetting", () => {
});
test("two rows, two colums", () => {
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'string[]' is not assignable to p... Remove this comment to see the full error message
const dfF = sourceDf.subset([0, 2], ["int32", "float32"]);
expect(dfF).toBeDefined();
expect(dfF.dims).toEqual([2, 2]);
@@ -236,6 +242,7 @@ describe("dataframe subsetting", () => {
expect(dfF.colIndex.labels()).toEqual(["int32", "float32"]);
// reverse the row and column order
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'string[]' is not assignable to p... Remove this comment to see the full error message
const dfFr = sourceDf.subset([2, 0], ["float32", "int32"]);
expect(dfFr).toBeDefined();
expect(dfFr.dims).toEqual([2, 2]);
@@ -248,6 +255,7 @@ describe("dataframe subsetting", () => {
test("withRowIndex", () => {
const df = sourceDf.subset(
null,
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'string[]' is not assignable to p... Remove this comment to see the full error message
["int32", "float32"],
new Dataframe.DenseInt32Index([3, 2, 1])
);
@@ -258,12 +266,15 @@ describe("dataframe subsetting", () => {
test("withRowIndex error checks", () => {
expect(() =>
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'string[]' is not assignable to p... Remove this comment to see the full error message
sourceDf.subset(null, ["red"], new Dataframe.IdentityInt32Index(1))
).toThrow(RangeError);
expect(() =>
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'string[]' is not assignable to p... Remove this comment to see the full error message
sourceDf.subset(null, ["red"], new Dataframe.DenseInt32Index([0, 1]))
).toThrow(RangeError);
expect(() =>
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'string[]' is not assignable to p... Remove this comment to see the full error message
sourceDf.subset(null, ["red"], new Dataframe.KeyIndex([0, 1, 2, 3]))
).toThrow(RangeError);
});
@@ -278,12 +289,14 @@ describe("dataframe subsetting", () => {
new Float32Array([4.4, 5.5, 6.6]),
["red", "green", "blue"],
],
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'DenseInt32Index' is not assignab... Remove this comment to see the full error message
new Dataframe.DenseInt32Index([2, 4, 6]),
new Dataframe.KeyIndex(["int32", "string", "float32", "colors"])
);
const dfA = sourceDf.isubsetMask(
new Uint8Array([0, 1, 1]),
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'Uint8Array' is not assignable to... Remove this comment to see the full error message
new Uint8Array([1, 0, 0, 1])
);
expect(dfA.dims).toEqual([2, 2]);
@@ -303,6 +316,7 @@ describe("dataframe subsetting", () => {
["red", "green", "blue"],
],
null, // identity index
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
new Dataframe.KeyIndex(["int32", "string", "float32", "colors"])
);
@@ -316,6 +330,7 @@ describe("dataframe subsetting", () => {
});
test("all rows, two cols", () => {
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'number[]' is not assignable to p... Remove this comment to see the full error message
const dfA = sourceDf.isubset(null, [1, 2]);
expect(dfA.dims).toEqual([3, 2]);
expect(dfA.icol(0).asArray()).toEqual(["A", "B", "C"]);
@@ -361,6 +376,7 @@ describe("dataframe factories", () => {
const dfA = new Dataframe.Dataframe(
[3, 2],
[new Int32Array([0, 1, 2]), new Int32Array([3, 4, 5])],
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'DenseInt32Index' is not assignab... Remove this comment to see the full error message
new Dataframe.DenseInt32Index([2, 1, 0]),
new Dataframe.KeyIndex(["A", "B"])
);
@@ -385,6 +401,7 @@ describe("dataframe factories", () => {
[true, false],
],
null,
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
new Dataframe.KeyIndex(["colors", "bools"])
);
const dfA = df.withCol("numbers", [1, 0]);
@@ -408,6 +425,7 @@ describe("dataframe factories", () => {
[true, false],
],
null,
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'DenseInt32Index' is not assignab... Remove this comment to see the full error message
new Dataframe.DenseInt32Index([74, 75])
);
const dfA = df.withCol(72, [1, 0]);
@@ -433,6 +451,7 @@ describe("dataframe factories", () => {
[true, false],
],
null,
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'DenseInt32Index' is not assignab... Remove this comment to see the full error message
new Dataframe.DenseInt32Index([74, 75])
);
const dfA = df.withCol(999, [1, 0]);
@@ -541,6 +560,7 @@ describe("dataframe factories", () => {
[1, 0],
],
null,
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
new Dataframe.KeyIndex(["colors", "bools", "numbers"])
);
@@ -549,11 +569,14 @@ describe("dataframe factories", () => {
[3, 1],
[["red", "blue", "green"]],
null,
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
new Dataframe.KeyIndex(["colorsA"])
);
// @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1.
expect(() => dfA.withColsFrom(dfB)).toThrow(RangeError);
/* duplicate labels should throw an error */
// @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1.
expect(() => dfA.withColsFrom(dfA)).toThrow(Error);
});
@@ -564,15 +587,18 @@ describe("dataframe factories", () => {
[2, 1],
[["red", "blue"]],
null,
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
new Dataframe.KeyIndex(["colors"])
);
const dfB = new Dataframe.Dataframe(
[2, 1],
[[true, false]],
null,
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
new Dataframe.KeyIndex(["bools"])
);
// @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1.
const dfLikeA = dfEmpty.withColsFrom(dfA);
expect(dfLikeA).toBeDefined();
expect(dfLikeA.dims).toEqual(dfA.dims);
@@ -581,6 +607,7 @@ describe("dataframe factories", () => {
expect(dfLikeA.rowIndex.labels()).toEqual(dfA.rowIndex.labels());
expect(dfLikeA.icol(0).asArray()).toEqual(dfA.icol(0).asArray());
// @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1.
const dfAlsoLikeA = dfA.withColsFrom(dfEmpty);
expect(dfAlsoLikeA).toBeDefined();
expect(dfAlsoLikeA.dims).toEqual(dfA.dims);
@@ -589,6 +616,7 @@ describe("dataframe factories", () => {
expect(dfAlsoLikeA.rowIndex.labels()).toEqual(dfA.rowIndex.labels());
expect(dfAlsoLikeA.icol(0).asArray()).toEqual(dfA.icol(0).asArray());
// @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1.
const dfC = dfA.withColsFrom(dfB);
expect(dfC).toBeDefined();
expect(dfC.dims).toEqual([2, 2]);
@@ -605,6 +633,7 @@ describe("dataframe factories", () => {
[2, 1],
[["red", "blue"]],
null,
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
new Dataframe.KeyIndex(["colors"])
);
const dfB = new Dataframe.Dataframe(
@@ -615,6 +644,7 @@ describe("dataframe factories", () => {
[1, 0],
],
null,
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
new Dataframe.KeyIndex(["colors", "bools", "numbers"])
);
@@ -647,6 +677,7 @@ describe("dataframe factories", () => {
[2, 1],
[["red", "blue"]],
null,
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
new Dataframe.KeyIndex(["colors"])
);
const dfB = new Dataframe.Dataframe(
@@ -657,6 +688,7 @@ describe("dataframe factories", () => {
[1, 0],
],
null,
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
new Dataframe.KeyIndex(["colors", "bools", "numbers"])
);
@@ -680,6 +712,7 @@ describe("dataframe factories", () => {
[1, 0],
],
null,
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
new Dataframe.KeyIndex(["colors", "bools", "numbers"])
);
const dfA = df.dropCol("colors");
@@ -751,6 +784,7 @@ describe("dataframe factories", () => {
[1, 0],
],
null,
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'DenseInt32Index' is not assignab... Remove this comment to see the full error message
new Dataframe.DenseInt32Index([102, 101, 100])
);
const dfA = df.dropCol(101);
@@ -777,7 +811,7 @@ describe("dataframe factories", () => {
new Float64Array(3).fill(1.1),
]
);
const dfB = dfA.mapColumns((col, idx) => {
const dfB = dfA.mapColumns((col: any, idx: any) => {
expect(dfA.icol(idx).asArray()).toBe(col);
return col;
});
@@ -822,6 +856,7 @@ describe("dataframe factories", () => {
[1, 0],
],
null,
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
new Dataframe.KeyIndex(["A", "B"])
);
const dfB = dfA.renameCol("B", "C");
@@ -834,7 +869,7 @@ describe("dataframe factories", () => {
});
describe("dataframe col", () => {
let df = null;
let df: any = null;
beforeEach(() => {
df = new Dataframe.Dataframe(
[2, 2],
@@ -843,6 +878,7 @@ describe("dataframe col", () => {
[1, 0],
],
null,
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
new Dataframe.KeyIndex(["A", "B"])
);
});
@@ -1195,6 +1231,7 @@ describe("label indexing", () => {
test("create", () => {
expect(Dataframe.isLabelIndex(idx)).toBeTruthy();
expect(() => new Dataframe.KeyIndex(["dup", "dup"])).toThrow(Error);
// @ts-expect-error ts-migrate(2554) FIXME: Expected 1 arguments, but got 0.
expect(new Dataframe.KeyIndex().size()).toEqual(0);
});
@@ -1367,6 +1404,7 @@ describe("corner cases", () => {
[1, 0],
],
null,
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
new Dataframe.KeyIndex(["A", "B"])
);
client/__tests__/util/dataframe/histogram.test.js → client/__tests__/util/dataframe/histogram.test.ts
+4
View File
@@ -6,6 +6,7 @@ describe("Dataframe column histogram", () => {
[3, 3],
[["n1", "n2", "n3"], ["c1", "c2", "c3"], new Int32Array([0, 1, 2])],
null,
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
new Dataframe.KeyIndex(["name", "cat", "value"])
);
@@ -26,6 +27,7 @@ describe("Dataframe column histogram", () => {
[3, 3],
[["n1", "n2", "n3"], ["c1", "c2", "c3"], new Int32Array([0, 1, 2])],
null,
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
new Dataframe.KeyIndex(["name", "cat", "value"])
);
@@ -48,6 +50,7 @@ describe("Dataframe column histogram", () => {
[3, 3],
[["n1", "n2", "n3"], ["c1", "c2", "c3"], new Int32Array([0, 1, 2])],
null,
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
new Dataframe.KeyIndex(["name", "cat", "value"])
);
@@ -68,6 +71,7 @@ describe("Dataframe column histogram", () => {
[3, 3],
[["n1", "n2", "n3"], ["c1", "c2", "c3"], new Int32Array([0, 1, 2])],
null,
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
new Dataframe.KeyIndex(["name", "cat", "value"])
);
client/__tests__/util/dataframe/summarize.test.js → client/__tests__/util/dataframe/summarize.test.ts
+6 -1
View File
@@ -1,6 +1,6 @@
import * as Dataframe from "../../../src/util/dataframe";
function float32Conversion(f) {
function float32Conversion(f: any) {
return new Float32Array([f])[0];
}
@@ -30,6 +30,7 @@ describe("Dataframe column summary", () => {
[1],
],
null,
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
new Dataframe.KeyIndex([
"name",
"nameString",
@@ -106,6 +107,7 @@ describe("Dataframe column summary", () => {
[1, false, "0"],
],
null,
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
new Dataframe.KeyIndex([
"name",
"nameString",
@@ -174,6 +176,7 @@ describe("Dataframe column summary", () => {
expect.objectContaining({
categorical: true,
categories: expect.arrayContaining([1, false, "0"]),
// @ts-expect-error ts-migrate(2769) FIXME: No overload matches this call.
categoryCounts: new Map([
[1, 1],
[false, 1],
@@ -201,6 +204,7 @@ describe("Dataframe column summary", () => {
[1, false, "0", "0"],
],
null,
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
new Dataframe.KeyIndex([
"name",
"nameString",
@@ -269,6 +273,7 @@ describe("Dataframe column summary", () => {
expect.objectContaining({
categorical: true,
categories: expect.arrayContaining([1, false, "0"]),
// @ts-expect-error ts-migrate(2769) FIXME: No overload matches this call.
categoryCounts: new Map([
[1, 1],
[false, 1],
client/__tests__/util/nameCreators.test.js → client/__tests__/util/nameCreators.test.ts
View File
client/__tests__/util/promiseLimit.test.js → client/__tests__/util/promiseLimit.test.ts
+3 -2
View File
@@ -1,7 +1,7 @@
import PromiseLimit from "../../src/util/promiseLimit";
import { range } from "../../src/util/range";
const delay = (t) => new Promise((resolve) => setTimeout(resolve, t));
const delay = (t: any) => new Promise((resolve) => setTimeout(resolve, t));
describe("PromiseLimit", () => {
test("simple evaluation, concurrency 1", async () => {
@@ -51,7 +51,8 @@ describe("PromiseLimit", () => {
running -= 1;
};
await Promise.all(range(10).map((i) => plimit.add(() => callback(i))));
// @ts-expect-error ts-migrate(2554) FIXME: Expected 3 arguments, but got 1.
await Promise.all(range(10).map((i: any) => plimit.add(() => callback(i))));
expect(maxRunning).toEqual(2);
});
client/__tests__/util/quantile.test.js → client/__tests__/util/quantile.test.ts
View File
client/__tests__/util/range.test.js → client/__tests__/util/range.test.ts
+6
View File
@@ -6,14 +6,20 @@ describe("range", () => {
});
test("range(stop)", () => {
// @ts-expect-error ts-migrate(2554) FIXME: Expected 3 arguments, but got 1.
expect(range(3)).toMatchObject([0, 1, 2]);
// @ts-expect-error ts-migrate(2554) FIXME: Expected 3 arguments, but got 1.
expect(range(0)).toMatchObject([]);
// @ts-expect-error ts-migrate(2554) FIXME: Expected 3 arguments, but got 1.
expect(range(1)).toMatchObject([0]);
});
test("range(start,stop)", () => {
// @ts-expect-error ts-migrate(2554) FIXME: Expected 3 arguments, but got 2.
expect(range(0, 0)).toMatchObject([]);
// @ts-expect-error ts-migrate(2554) FIXME: Expected 3 arguments, but got 2.
expect(range(0, 2)).toMatchObject([0, 1]);
// @ts-expect-error ts-migrate(2554) FIXME: Expected 3 arguments, but got 2.
expect(range(4, 8)).toMatchObject([4, 5, 6, 7]);
});
client/__tests__/util/stateManager/colorHelpers.test.js → client/__tests__/util/stateManager/colorHelpers.test.ts
+13 -8
View File
@@ -81,6 +81,7 @@ describe("categorical color helpers", () => {
),
],
null,
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
new Dataframe.KeyIndex(["continuousColumn", "categoricalColumn"])
);
@@ -95,6 +96,7 @@ describe("categorical color helpers", () => {
const data = obsDataframe.col("categoricalColumn").asArray();
const cats = schema.annotations.obsByName.categoricalColumn.categories;
for (let i = 0; i < schema.dataframe.nObs; i += 1) {
// @ts-expect-error ts-migrate(2722) FIXME: Cannot invoke an object which is possibly 'undefin... Remove this comment to see the full error message
expect(makeScale(ct.rgb[i])).toEqual(ct.scale(cats.indexOf(data[i])));
}
});
@@ -112,6 +114,7 @@ describe("categorical color helpers", () => {
const data = obsDataframe.col("categoricalColumn").asArray();
const cats = schemaClone.annotations.obsByName.categoricalColumn.categories;
for (let i = 0; i < schemaClone.dataframe.nObs; i += 1) {
// @ts-expect-error ts-migrate(2722) FIXME: Cannot invoke an object which is possibly 'undefin... Remove this comment to see the full error message
expect(makeScale(ct.rgb[i])).toEqual(ct.scale(cats.indexOf(data[i])));
}
});
@@ -122,7 +125,7 @@ describe("categorical color helpers", () => {
Array.from(schema.annotations.obsByName.categoricalColumn.categories)
);
const userDefinedColorTable = {
categoricalColumn: shuffleCats.reduce((acc, label) => {
categoricalColumn: shuffleCats.reduce((acc: any, label: any) => {
acc[label] = randRGBColor();
return acc;
}, {}),
@@ -136,12 +139,14 @@ describe("categorical color helpers", () => {
"categoricalColumn",
obsDataframe,
schema,
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type '{}' is not assignable to paramet... Remove this comment to see the full error message
userColors
);
expect(ct).toBeDefined();
const data = obsDataframe.col("categoricalColumn").asArray();
for (let i = 0; i < schema.dataframe.nObs; i += 1) {
expect(makeScale(ct.rgb[i])).toEqual(
// @ts-expect-error ts-migrate(2722) FIXME: Cannot invoke an object which is possibly 'undefin... Remove this comment to see the full error message
ct.scale(cats.indexOf(data[i])).toString()
);
}
@@ -154,31 +159,31 @@ TODO:
2. user defined colors
*/
function indexSchema(schema) {
function indexSchema(schema: any) {
schema.annotations.obsByName = Object.fromEntries(
schema.annotations?.obs?.columns?.map((v) => [v.name, v]) ?? []
schema.annotations?.obs?.columns?.map((v: any) => [v.name, v]) ?? []
);
schema.annotations.varByName = Object.fromEntries(
schema.annotations?.var?.columns?.map((v) => [v.name, v]) ?? []
schema.annotations?.var?.columns?.map((v: any) => [v.name, v]) ?? []
);
schema.layout.obsByName = Object.fromEntries(
schema.layout?.obs?.map((v) => [v.name, v]) ?? []
schema.layout?.obs?.map((v: any) => [v.name, v]) ?? []
);
schema.layout.varByName = Object.fromEntries(
schema.layout?.var?.map((v) => [v.name, v]) ?? []
schema.layout?.var?.map((v: any) => [v.name, v]) ?? []
);
return schema;
}
function makeScale(rgb) {
function makeScale(rgb: any) {
// make a scale string from a rgb float triple
return `rgb(${(rgb[0] * 255) >>> 0}, ${(rgb[1] * 255) >>> 0}, ${
(rgb[2] * 256) >>> 0
})`;
}
function shuffle(array) {
function shuffle(array: any) {
for (let i = array.length - 1; i > 0; i -= 1) {
const j = (Math.random() * (i + 1)) >>> 0;
[array[i], array[j]] = [array[j], array[i]];
client/__tests__/util/stateManager/controlsHelpers.test.js → client/__tests__/util/stateManager/controlsHelpers.test.ts
View File
client/__tests__/util/stateManager/fbs.test.js → client/__tests__/util/stateManager/fbs.test.ts
+1
View File
@@ -24,6 +24,7 @@ describe("encode/decode", () => {
expect(dfA.columns).toEqual(columns);
const colIndex = new KeyIndex(["a", "b", "c", "d"]);
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message
const dfWithColIdx = new Dataframe([3, 4], columns, null, colIndex);
const dfB = decodeMatrixFBS(encodeMatrixFBS(dfWithColIdx));
expect([dfB.nRows, dfB.nCols]).toEqual(dfWithColIdx.dims);
client/__tests__/util/stateManager/sampleResponses.js → client/__tests__/util/stateManager/sampleResponses.ts
+9 -2
View File
@@ -75,6 +75,7 @@ const aSchemaResponse = {
const anAnnotationsObsJSONResponse = {
names: ["name", "field1", "field2", "field3", "field4"],
// @ts-expect-error ts-migrate(2554) FIXME: Expected 1 arguments, but got 0.
data: _()
.range(nObs)
.map((idx) => [
@@ -91,6 +92,7 @@ const anAnnotationsObsJSONResponse = {
const anAnnotationsVarJSONResponse = {
names: ["fieldA", "fieldB", "fieldC", "fieldD", "name"],
// @ts-expect-error ts-migrate(2554) FIXME: Expected 1 arguments, but got 0.
data: _()
.range(nVar)
.map((idx) => [
@@ -105,7 +107,7 @@ const anAnnotationsVarJSONResponse = {
.value(),
};
function encodeTypedArray(builder, uType, uData) {
function encodeTypedArray(builder: any, uType: any, uData: any) {
const uTypeName = NetEncoding.TypedArray[uType];
const ArrayType = NetEncoding[uTypeName];
const dv = ArrayType.createDataVector(builder, uData);
@@ -114,7 +116,7 @@ function encodeTypedArray(builder, uType, uData) {
return builder.endObject();
}
function encodeMatrix(columns, colIndex = undefined) {
function encodeMatrix(columns: any, colIndex = undefined) {
/*
IMPORTANT: this is not a general purpose encoder. in particular,
it doesn't correctly handle all column index types, nor does it
@@ -123,6 +125,7 @@ function encodeMatrix(columns, colIndex = undefined) {
encodeMatrixFBS in matrix.py is more general. This is used only
as a testing santity check (alt implementation).
*/
// @ts-expect-error ts-migrate(2554) FIXME: Expected 0 arguments, but got 1.
const utf8Encoder = new TextEncoder("utf-8");
const builder = new flatbuffers.Builder(1024);
const cols = map(columns, (carr) => {
@@ -172,11 +175,13 @@ function encodeMatrix(columns, colIndex = undefined) {
const anAnnotationsObsFBSResponse = (() => {
const columns = zip(...anAnnotationsObsJSONResponse.data).slice(1);
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'string[]' is not assignable to p... Remove this comment to see the full error message
return encodeMatrix(columns, anAnnotationsObsJSONResponse.names);
})();
const anAnnotationsVarFBSResponse = (() => {
const columns = zip(...anAnnotationsVarJSONResponse.data).slice(1);
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'string[]' is not assignable to p... Remove this comment to see the full error message
return encodeMatrix(columns, anAnnotationsVarJSONResponse.names);
})();
@@ -185,11 +190,13 @@ const aLayoutFBSResponse = (() => {
new Float32Array(nObs).fill(Math.random()),
new Float32Array(nObs).fill(Math.random()),
];
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'string[]' is not assignable to p... Remove this comment to see the full error message
return encodeMatrix(coords, ["umap_0", "umap_1"]);
})();
const aDataObsResponse = {
var: [2, 4, 29],
// @ts-expect-error ts-migrate(2554) FIXME: Expected 1 arguments, but got 0.
obs: _()
.range(nObs)
.map((idx) => [idx, Math.random(), Math.random(), Math.random()])
client/__tests__/util/typedCrossfilter/bitArray.test.js → client/__tests__/util/typedCrossfilter/bitArray.test.ts
View File
client/__tests__/util/typedCrossfilter/crossfilter.test.js → client/__tests__/util/typedCrossfilter/crossfilter.test.ts
+46 -16
View File
@@ -126,7 +126,7 @@ const someData = [
},
];
let payments = null;
let payments: any = null;
beforeEach(() => {
payments = new Crossfilter(someData);
});
@@ -138,7 +138,12 @@ describe("ImmutableTypedCrossfilter", () => {
expect(payments.all()).toEqual(someData);
const p = payments
.addDimension("quantity", "scalar", (i, d) => d[i].quantity, Int32Array)
.addDimension(
"quantity",
"scalar",
(i: any, d: any) => d[i].quantity,
Int32Array
)
.select("quantity", { mode: "all" });
expect(p).toBeDefined();
expect(p.all()).toEqual(someData);
@@ -158,7 +163,7 @@ describe("ImmutableTypedCrossfilter", () => {
const p2 = payments.addDimension(
"quantity",
"scalar",
(i, data) => data[i].quantity,
(i: any, data: any) => data[i].quantity,
Int32Array
);
@@ -175,10 +180,20 @@ describe("ImmutableTypedCrossfilter", () => {
test("select all and none", () => {
let p = payments
.addDimension("quantity", "scalar", (i, d) => d[i].quantity, Int32Array)
.addDimension("tip", "scalar", (i, d) => d[i].tip, Float32Array)
.addDimension("total", "scalar", (i, d) => d[i].total, Float32Array)
.addDimension("type", "enum", (i, d) => d[i].type);
.addDimension(
"quantity",
"scalar",
(i: any, d: any) => d[i].quantity,
Int32Array
)
.addDimension("tip", "scalar", (i: any, d: any) => d[i].tip, Float32Array)
.addDimension(
"total",
"scalar",
(i: any, d: any) => d[i].total,
Float32Array
)
.addDimension("type", "enum", (i: any, d: any) => d[i].type);
expect(p).toBeDefined();
/* expect all records to be selected - default init state */
@@ -230,11 +245,21 @@ describe("ImmutableTypedCrossfilter", () => {
});
describe("scalar dimension", () => {
let p;
let p: any;
beforeEach(() => {
p = payments
.addDimension("quantity", "scalar", (i, d) => d[i].quantity, Int32Array)
.addDimension("tip", "scalar", (i, d) => d[i].tip, Float32Array)
.addDimension(
"quantity",
"scalar",
(i: any, d: any) => d[i].quantity,
Int32Array
)
.addDimension(
"tip",
"scalar",
(i: any, d: any) => d[i].tip,
Float32Array
)
.select("tip", { mode: "all" });
});
@@ -277,9 +302,9 @@ describe("ImmutableTypedCrossfilter", () => {
});
describe("enum dimension", () => {
let p;
let p: any;
beforeEach(() => {
p = payments.addDimension("type", "enum", (i, d) => d[i].type);
p = payments.addDimension("type", "enum", (i: any, d: any) => d[i].type);
});
test("all", () => {
@@ -317,7 +342,7 @@ describe("ImmutableTypedCrossfilter", () => {
});
describe("spatial dimension", () => {
let p;
let p: any;
beforeEach(() => {
const X = someData.map((r) => r.coords[0]);
const Y = someData.map((r) => r.coords[1]);
@@ -406,14 +431,19 @@ describe("ImmutableTypedCrossfilter", () => {
});
describe("non-finite scalars", () => {
let p;
let p: any;
beforeEach(() => {
p = payments
.addDimension("quantity", "scalar", (i, d) => d[i].quantity, Int32Array)
.addDimension(
"quantity",
"scalar",
(i: any, d: any) => d[i].quantity,
Int32Array
)
.addDimension(
"nonFinite",
"scalar",
(i, d) => d[i].nonFinite,
(i: any, d: any) => d[i].nonFinite,
Float32Array
)
.select("quantity", { mode: "all" });
client/__tests__/util/typedCrossfilter/positiveInterval.test.js → client/__tests__/util/typedCrossfilter/positiveInterval.test.ts
View File
client/__tests__/util/typedCrossfilter/sort.test.js → client/__tests__/util/typedCrossfilter/sort.test.ts
+13 -5
View File
@@ -15,7 +15,7 @@ paths for:
const pInf = Number.POSITIVE_INFINITY;
const nInf = Number.NEGATIVE_INFINITY;
function fillRange(arr, start = 0) {
function fillRange(arr: any, start = 0) {
const larr = arr;
for (let i = 0, len = larr.length; i < len; i += 1) {
larr[i] = i + start;
@@ -23,7 +23,7 @@ function fillRange(arr, start = 0) {
return larr;
}
function fillRand(arr) {
function fillRand(arr: any) {
for (let i = 0, len = arr.length; i < len; i += 1) {
arr[i] = Math.random();
}
@@ -48,16 +48,22 @@ describe("sortArray", () => {
describe("finite numbers", () => {
[Array, Float32Array, Uint32Array, Int32Array, Float64Array].map((Type) =>
test(Type.name, () => {
// @ts-expect-error ts-migrate(2349) FIXME: This expression is not callable.
expect(sortArray(Type.from([6, 5, 4, 3, 2, 1, 0]))).toMatchObject(
// @ts-expect-error ts-migrate(2349) FIXME: This expression is not callable.
Type.from([0, 1, 2, 3, 4, 5, 6])
);
// @ts-expect-error ts-migrate(2349) FIXME: This expression is not callable.
expect(sortArray(Type.from([6, 5, 4, 3, 2, 1]))).toMatchObject(
// @ts-expect-error ts-migrate(2349) FIXME: This expression is not callable.
Type.from([1, 2, 3, 4, 5, 6])
);
const source = fillRand(new Type(1000));
// @ts-expect-error ts-migrate(2349) FIXME: This expression is not callable.
expect(sortArray(Type.from(source))).toMatchObject(
// @ts-expect-error ts-migrate(2349) FIXME: This expression is not callable.
Type.from(source).sort()
);
})
@@ -130,22 +136,24 @@ describe("sortIndex", () => {
describe("finite numbers", () => {
[Array, Float32Array, Uint32Array, Int32Array, Float64Array].map((Type) =>
test(Type.name, () => {
// @ts-expect-error ts-migrate(2349) FIXME: This expression is not callable.
const source1 = Type.from([6, 5, 4, 3, 2, 1, 0]);
const index1 = fillRange(new Uint32Array(source1.length));
expect(sortIndex(index1, source1)).toMatchObject(
index1.sort((a, b) => source1[a] - source1[b])
index1.sort((a: any, b: any) => source1[a] - source1[b])
);
// @ts-expect-error ts-migrate(2349) FIXME: This expression is not callable.
const source2 = Type.from([6, 5, 4, 3, 2, 1]);
const index2 = fillRange(new Uint32Array(source2.length));
expect(sortIndex(index2, source2)).toMatchObject(
index2.sort((a, b) => source1[a] - source1[b])
index2.sort((a: any, b: any) => source1[a] - source1[b])
);
const source3 = fillRand(new Type(1000));
const index3 = fillRange(new Uint32Array(source3.length));
expect(sortIndex(index3, source3)).toMatchObject(
index3.sort((a, b) => source1[a] - source1[b])
index3.sort((a: any, b: any) => source1[a] - source1[b])
);
})
);
client/__tests__/util/typedCrossfilter/util.test.js → client/__tests__/util/typedCrossfilter/util.test.ts
View File
client/configuration/babel/babel.dev.js
+1
View File
@@ -11,6 +11,7 @@ module.exports = {
},
],
"@babel/preset-react",
"@babel/preset-typescript",
],
plugins: [
"@babel/plugin-proposal-function-bind",
client/configuration/babel/babel.prod.js
+1
View File
@@ -10,6 +10,7 @@ module.exports = {
},
],
"@babel/preset-react",
"@babel/preset-typescript"
],
plugins: [
"@babel/plugin-proposal-function-bind",
client/configuration/eslint/eslint.js
+34 -5
View File
@@ -1,13 +1,12 @@
module.exports = {
root: true,
parser: "babel-eslint",
parser: "@typescript-eslint/parser",
extends: [
"airbnb",
"airbnb-typescript",
"plugin:eslint-comments/recommended",
"plugin:@blueprintjs/recommended",
"plugin:compat/recommended",
"plugin:prettier/recommended",
"prettier",
],
settings: {
// AbortController is not supported in iOS Safari 10.3, Chrome 61
@@ -32,18 +31,47 @@ module.exports = {
jsx: true,
generators: true,
},
project: "./tsconfig.json",
},
rules: {
"react/jsx-no-target-blank": "off",
"eslint-comments/require-description": ["error"],
"no-magic-numbers": "off",
"@typescript-eslint/no-magic-numbers": "off",
"no-nested-ternary": "off",
"func-style": "off",
"arrow-parens": "off",
"no-use-before-define": "off",
"@typescript-eslint/no-use-before-define": "off",
"react/jsx-filename-extension": "off",
"comma-dangle": "off",
"@typescript-eslint/comma-dangle": "off",
"no-underscore-dangle": "off",
// Override airbnb config to allow leading underscore
// https://github.com/iamturns/eslint-config-airbnb-typescript/blob/master/lib/shared.js#L35
"@typescript-eslint/naming-convention": [
"error",
{
selector: "class",
format: ["PascalCase"],
leadingUnderscore: "allow",
},
{
selector: "function",
format: ["camelCase", "PascalCase"],
leadingUnderscore: "allowSingleOrDouble",
},
{
selector: "typeLike",
format: ["PascalCase"],
},
{
selector: "variable",
format: ["camelCase", "PascalCase", "UPPER_CASE"],
leadingUnderscore: "allowSingleOrDouble",
trailingUnderscore: "allowDouble",
},
],
"implicit-arrow-linebreak": "off",
"no-console": "off",
"spaced-comment": ["error", "always", { exceptions: ["*"] }],
@@ -51,6 +79,7 @@ module.exports = {
"object-curly-newline": ["error", { consistent: true }],
"react/prop-types": [0],
"space-before-function-paren": "off",
"@typescript-eslint/space-before-function-paren": "off",
"function-paren-newline": "off",
"prefer-destructuring": ["error", { object: true, array: false }],
"import/prefer-default-export": "off",
@@ -69,9 +98,9 @@ module.exports = {
},
overrides: [
{
files: ["**/*.test.js"],
files: ["**/*.test.ts"],
env: {
jest: true, // now **/*.test.js files' env has both es6 *and* jest
jest: true, // now **/*.test.ts files' env has both es6 *and* jest
},
// Can't extend in overrides: https://github.com/eslint/eslint/issues/8813
// "extends": ["plugin:jest/recommended"]
client/configuration/lint-staged/lint-staged.config.js
+1 -1
View File
@@ -1,3 +1,3 @@
module.exports = {
"*.js": "eslint --fix",
"*.{js,ts,jsx,tsx}": "eslint --fix",
};
client/configuration/webpack/webpack.config.dev.js
+1 -1
View File
@@ -23,7 +23,7 @@ const devConfig = {
module: {
rules: [
{
test: /\.jsx?$/,
test: /\.(ts|js)x?$/,
loader: "babel-loader",
options: babelOptions,
},
client/configuration/webpack/webpack.config.prod.js
+1 -1
View File
@@ -38,7 +38,7 @@ const prodConfig = {
module: {
rules: [
{
test: /\.jsx?$/,
test: /\.(ts|js)x?$/,
loader: "babel-loader",
options: babelOptions,
},
client/configuration/webpack/webpack.config.shared.js
+3
View File
@@ -29,6 +29,9 @@ module.exports = {
path: path.resolve("build"),
publicPath,
},
resolve: {
extensions: [".ts", ".tsx", "..."],
},
module: {
rules: [
{
client/package-lock.json
Generated
+1612 -388
View File
File diff suppressed because it is too large Load Diff
client/package.json
+37 -7
View File
@@ -8,9 +8,9 @@
"build": "npm run clean && webpack --config",
"clean": "rimraf build",
"dev": "npm run build -- configuration/webpack/webpack.config.dev.js",
"e2e": "jest --config __tests__/e2e/e2eJestConfig.json e2e/e2e.test.js",
"e2e-annotations": "jest --config __tests__/e2e/e2eJestConfig.json e2e/e2eAnnotations.test.js",
"e2e-prod": "CXG_URL_BASE='https://cellxgene.cziscience.com/d/pbmc3k.cxg/' jest --config __tests__/e2e/e2eJestConfig.json e2e/e2e.test.js",
"e2e": "jest --config __tests__/e2e/e2eJestConfig.json e2e/e2e.test.ts",
"e2e-annotations": "jest --config __tests__/e2e/e2eJestConfig.json e2e/e2eAnnotations.test.ts",
"e2e-prod": "CXG_URL_BASE='https://cellxgene.cziscience.com/d/pbmc3k.cxg/' jest --config __tests__/e2e/e2eJestConfig.json e2e/e2e.test.ts",
"fmt": "eslint --fix src __tests__",
"lint": "eslint --fix src __tests__",
"prod": "npm run build -- configuration/webpack/webpack.config.prod.js",
@@ -90,10 +90,38 @@
"@babel/plugin-transform-runtime": "^7.13.15",
"@babel/preset-env": "^7.13.15",
"@babel/preset-react": "^7.13.13",
"@babel/preset-typescript": "^7.14.5",
"@babel/register": "^7.13.16",
"@babel/runtime": "^7.13.16",
"@blueprintjs/eslint-plugin": "^0.3.0",
"@sentry/webpack-plugin": "^1.15.0",
"@types/d3": "^7.0.0",
"@types/d3-scale-chromatic": "^3.0.0",
"@types/expect-puppeteer": "^4.4.6",
"@types/flatbuffers": "^1.10.0",
"@types/is-number": "^7.0.1",
"@types/jest": "^26.0.24",
"@types/jest-environment-puppeteer": "^4.4.1",
"@types/lodash.clonedeep": "^4.5.6",
"@types/lodash.difference": "^4.5.6",
"@types/lodash.every": "^4.6.6",
"@types/lodash.filter": "^4.6.6",
"@types/lodash.foreach": "^4.5.6",
"@types/lodash.isnumber": "^3.0.6",
"@types/lodash.map": "^4.6.13",
"@types/lodash.pull": "^4.1.6",
"@types/lodash.sortby": "^4.7.6",
"@types/lodash.uniq": "^4.5.6",
"@types/lodash.zip": "^4.2.6",
"@types/pako": "^1.0.2",
"@types/puppeteer": "^5.4.4",
"@types/react": "^17.0.14",
"@types/react-dom": "^17.0.9",
"@types/react-helmet": "^6.1.2",
"@types/react-redux": "^7.1.18",
"@types/sha1": "^1.1.3",
"@typescript-eslint/eslint-plugin": "^4.28.4",
"@typescript-eslint/parser": "^4.28.4",
"babel-eslint": "^10.1.0",
"babel-jest": "^26.1.0",
"babel-loader": "^8.1.0",
@@ -106,7 +134,7 @@
"connect-history-api-fallback": "^1.6.0",
"css-loader": "^5.2.4",
"eslint": "^7.24.0",
"eslint-config-airbnb": "^18.2.0",
"eslint-config-airbnb-typescript": "^12.3.1",
"eslint-config-prettier": "^8.2.0",
"eslint-loader": "^4.0.2",
"eslint-plugin-compat": "^3.8.0",
@@ -149,6 +177,7 @@
"style-loader": "^2.0.0",
"sw-precache-webpack-plugin": "^1.0.0",
"terser-webpack-plugin": "^5.1.1",
"typescript": "^4.3.5",
"url-loader": "^4.1.0",
"webpack": "^5.34.0",
"webpack-cli": "^4.6.0",
@@ -157,10 +186,10 @@
},
"jest": {
"testMatch": [
"**/__tests__/**/?(*.)(spec|test).js?(x)"
"**/__tests__/**/?(*.)(spec|test).ts?(x)"
],
"setupFiles": [
"./__tests__/setupMissingGlobals.js"
"./__tests__/setupMissingGlobals.ts"
],
"coverageDirectory": "./coverage/",
"collectCoverage": true
@@ -170,7 +199,8 @@
"test": {
"presets": [
"@babel/preset-env",
"@babel/preset-react"
"@babel/preset-react",
"@babel/preset-typescript"
],
"plugins": [
"@babel/plugin-proposal-function-bind",
client/src/actions/annotation.js → client/src/actions/annotation.ts
+40 -31
View File
@@ -9,9 +9,9 @@ import { MatrixFBS, AnnotationsHelpers } from "../util/stateManager";
const { isUserAnnotation } = AnnotationsHelpers;
export const annotationCreateCategoryAction = (
newCategoryName,
categoryToDuplicate
) => async (dispatch, getState) => {
newCategoryName: any,
categoryToDuplicate: any
) => async (dispatch: any, getState: any) => {
/*
Add a new user-created category to the obs annotations.
@@ -89,9 +89,9 @@ export const annotationCreateCategoryAction = (
};
export const annotationRenameCategoryAction = (
oldCategoryName,
newCategoryName
) => (dispatch, getState) => {
oldCategoryName: any,
newCategoryName: any
) => (dispatch: any, getState: any) => {
/*
Rename a user-created annotation category
*/
@@ -124,9 +124,9 @@ export const annotationRenameCategoryAction = (
});
};
export const annotationDeleteCategoryAction = (categoryName) => (
dispatch,
getState
export const annotationDeleteCategoryAction = (categoryName: any) => (
dispatch: any,
getState: any
) => {
/*
Delete a user-created category
@@ -149,10 +149,10 @@ export const annotationDeleteCategoryAction = (categoryName) => (
};
export const annotationCreateLabelInCategory = (
categoryName,
labelName,
assignSelected
) => async (dispatch, getState) => {
categoryName: any,
labelName: any,
assignSelected: any
) => async (dispatch: any, getState: any) => {
/*
Add a new label to a user-defined category. If assignSelected is true, assign
the label to all currently selected cells.
@@ -188,9 +188,9 @@ export const annotationCreateLabelInCategory = (
};
export const annotationDeleteLabelFromCategory = (
categoryName,
labelName
) => async (dispatch, getState) => {
categoryName: any,
labelName: any
) => async (dispatch: any, getState: any) => {
/*
delete a label from a user-defined category
*/
@@ -218,10 +218,10 @@ export const annotationDeleteLabelFromCategory = (
};
export const annotationRenameLabelInCategory = (
categoryName,
oldLabelName,
newLabelName
) => async (dispatch, getState) => {
categoryName: any,
oldLabelName: any,
newLabelName: any
) => async (dispatch: any, getState: any) => {
/*
label name change
*/
@@ -255,9 +255,9 @@ export const annotationRenameLabelInCategory = (
};
export const annotationLabelCurrentSelection = (
categoryName,
labelName
) => async (dispatch, getState) => {
categoryName: any,
labelName: any
) => async (dispatch: any, getState: any) => {
/*
set the label on all currently selected
*/
@@ -284,13 +284,16 @@ export const annotationLabelCurrentSelection = (
});
};
function writableAnnotations(annoMatrix) {
function writableAnnotations(annoMatrix: any) {
return annoMatrix.schema.annotations.obs.columns
.filter((s) => s.writable)
.map((s) => s.name);
.filter((s: any) => s.writable)
.map((s: any) => s.name);
}
export const needToSaveObsAnnotations = (annoMatrix, lastSavedAnnoMatrix) => {
export const needToSaveObsAnnotations = (
annoMatrix: any,
lastSavedAnnoMatrix: any
) => {
/*
Return true if there are LIKELY user-defined annotation modifications between the two
annoMatrices. Technically not an action creator, but intimately intertwined
@@ -314,11 +317,14 @@ export const needToSaveObsAnnotations = (annoMatrix, lastSavedAnnoMatrix) => {
// no schema changes; check for change in contents
return currentWritable.some(
(col) => annoMatrix.col(col) !== lastSavedAnnoMatrix.col(col)
(col: any) => annoMatrix.col(col) !== lastSavedAnnoMatrix.col(col)
);
};
export const saveObsAnnotationsAction = () => async (dispatch, getState) => {
export const saveObsAnnotationsAction = () => async (
dispatch: any,
getState: any
) => {
/*
Save the user-created obs annotations IF any have changed.
*/
@@ -388,7 +394,10 @@ export const saveObsAnnotationsAction = () => async (dispatch, getState) => {
}
};
export const saveGenesetsAction = () => async (dispatch, getState) => {
export const saveGenesetsAction = () => async (
dispatch: any,
getState: any
) => {
const state = getState();
// bail if gene sets not available, or in readonly mode.
@@ -465,7 +474,7 @@ export const saveGenesetsAction = () => async (dispatch, getState) => {
res,
});
}
return Promise.all([
return await Promise.all([
dispatch({
type: "autosave: genesets complete",
lastSavedGenesets: genesets,
client/src/actions/embedding.js → client/src/actions/embedding.ts
+6 -6
View File
@@ -6,9 +6,9 @@ import { AnnoMatrixObsCrossfilter } from "../annoMatrix";
import { _setEmbeddingSubset } from "../util/stateManager/viewStackHelpers";
export async function _switchEmbedding(
prevAnnoMatrix,
prevCrossfilter,
newEmbeddingName
prevAnnoMatrix: any,
prevCrossfilter: any,
newEmbeddingName: any
) {
/*
DRY helper used by embedding action creators
@@ -25,9 +25,9 @@ export async function _switchEmbedding(
return [annoMatrix, obsCrossfilter];
}
export const layoutChoiceAction = (newLayoutChoice) => async (
dispatch,
getState
export const layoutChoiceAction = (newLayoutChoice: any) => async (
dispatch: any,
getState: any
) => {
/*
On layout choice, make sure we have selected all on the previous layout, AND the new
client/src/actions/geneset.js → client/src/actions/geneset.ts
+26 -13
View File
@@ -21,7 +21,10 @@ The behavior manifest in these action creators:
Note that crossfilter indices are lazy created, as needed.
*/
export const genesetDelete = (genesetName) => (dispatch, getState) => {
export const genesetDelete = (genesetName: any) => (
dispatch: any,
getState: any
) => {
const state = getState();
const { genesets } = state;
const gs = genesets?.genesets?.get(genesetName) ?? {};
@@ -40,9 +43,9 @@ export const genesetDelete = (genesetName) => (dispatch, getState) => {
});
};
export const genesetAddGenes = (genesetName, genes) => async (
dispatch,
getState
export const genesetAddGenes = (genesetName: any, genes: any) => async (
dispatch: any,
getState: any
) => {
const state = getState();
const { obsCrossfilter: prevObsCrossfilter, annoMatrix } = state;
@@ -50,7 +53,7 @@ export const genesetAddGenes = (genesetName, genes) => async (
const varIndex = schema.annotations.var.index;
const df = await annoMatrix.fetch("var", varIndex);
const geneNames = df.col(varIndex).asArray();
genes = genes.reduce((acc, gene) => {
genes = genes.reduce((acc: any, gene: any) => {
if (geneNames.indexOf(gene.geneSymbol) === -1) {
postUserErrorToast(
`${gene.geneSymbol} doesn't appear to be a valid gene name.`
@@ -78,9 +81,9 @@ export const genesetAddGenes = (genesetName, genes) => async (
});
};
export const genesetDeleteGenes = (genesetName, geneSymbols) => (
dispatch,
getState
export const genesetDeleteGenes = (genesetName: any, geneSymbols: any) => (
dispatch: any,
getState: any
) => {
const state = getState();
const obsCrossfilter = dropGeneset(dispatch, state, genesetName, geneSymbols);
@@ -97,7 +100,11 @@ export const genesetDeleteGenes = (genesetName, geneSymbols) => (
Private
*/
function dropGenesetSummaryDimension(obsCrossfilter, state, genesetName) {
function dropGenesetSummaryDimension(
obsCrossfilter: any,
state: any,
genesetName: any
) {
const { annoMatrix, genesets } = state;
const varIndex = annoMatrix.schema.annotations?.var?.index;
const gs = genesets?.genesets?.get(genesetName) ?? {};
@@ -113,7 +120,7 @@ function dropGenesetSummaryDimension(obsCrossfilter, state, genesetName) {
return obsCrossfilter.dropDimension("X", query);
}
function dropGeneDimension(obsCrossfilter, state, gene) {
function dropGeneDimension(obsCrossfilter: any, state: any, gene: any) {
const { annoMatrix } = state;
const varIndex = annoMatrix.schema.annotations?.var?.index;
const query = {
@@ -126,10 +133,16 @@ function dropGeneDimension(obsCrossfilter, state, gene) {
return obsCrossfilter.dropDimension("X", query);
}
function dropGeneset(dispatch, state, genesetName, geneSymbols) {
function dropGeneset(
dispatch: any,
state: any,
genesetName: any,
geneSymbols: any
) {
const { obsCrossfilter: prevObsCrossfilter } = state;
const obsCrossfilter = geneSymbols.reduce(
(crossfilter, gene) => dropGeneDimension(crossfilter, state, gene),
(crossfilter: any, gene: any) =>
dropGeneDimension(crossfilter, state, gene),
dropGenesetSummaryDimension(prevObsCrossfilter, state, genesetName)
);
dispatch({
@@ -137,7 +150,7 @@ function dropGeneset(dispatch, state, genesetName, geneSymbols) {
continuousNamespace: { isGeneSetSummary: true },
selection: genesetName,
});
geneSymbols.forEach((g) =>
geneSymbols.forEach((g: any) =>
dispatch({
type: "continuous metadata histogram cancel",
continuousNamespace: { isUserDefined: true },
client/src/actions/index.js → client/src/actions/index.ts
+22 -18
View File
@@ -15,7 +15,7 @@ import * as genesetActions from "./geneset";
/*
return promise fetching user-configured colors
*/
async function userColorsFetchAndLoad(dispatch) {
async function userColorsFetchAndLoad(dispatch: any) {
return fetchJson("colors").then((response) =>
dispatch({
type: "universe: user color load success",
@@ -28,7 +28,7 @@ async function schemaFetch() {
return fetchJson("schema");
}
async function configFetch(dispatch) {
async function configFetch(dispatch: any) {
return fetchJson("config").then((response) => {
const config = { ...globals.configDefaults, ...response.config };
dispatch({
@@ -39,7 +39,7 @@ async function configFetch(dispatch) {
});
}
async function userInfoFetch(dispatch) {
async function userInfoFetch(dispatch: any) {
return fetchJson("userinfo").then((response) => {
const { userinfo: userInfo } = response || {};
dispatch({
@@ -50,7 +50,7 @@ async function userInfoFetch(dispatch) {
});
}
async function genesetsFetch(dispatch, config) {
async function genesetsFetch(dispatch: any, config: any) {
/* request genesets ONLY if the backend supports the feature */
const defaultResponse = {
genesets: [],
@@ -71,25 +71,26 @@ async function genesetsFetch(dispatch, config) {
}
}
function prefetchEmbeddings(annoMatrix) {
function prefetchEmbeddings(annoMatrix: any) {
/*
prefetch requests for all embeddings
*/
const { schema } = annoMatrix;
const available = schema.layout.obs.map((v) => v.name);
available.forEach((embName) => annoMatrix.prefetch("emb", embName));
const available = schema.layout.obs.map((v: any) => v.name);
available.forEach((embName: any) => annoMatrix.prefetch("emb", embName));
}
/*
Application bootstrap
*/
const doInitialDataLoad = () =>
catchErrorsWrap(async (dispatch) => {
catchErrorsWrap(async (dispatch: any) => {
dispatch({ type: "initial data load start" });
try {
const [config, schema] = await Promise.all([
configFetch(dispatch),
// @ts-expect-error ts-migrate(2554) FIXME: Expected 0 arguments, but got 1.
schemaFetch(dispatch),
userColorsFetchAndLoad(dispatch),
userInfoFetch(dispatch),
@@ -113,7 +114,7 @@ const doInitialDataLoad = () =>
const layoutSchema = schema?.schema?.layout?.obs ?? [];
if (
defaultEmbedding &&
layoutSchema.some((s) => s.name === defaultEmbedding)
layoutSchema.some((s: any) => s.name === defaultEmbedding)
) {
dispatch(embActions.layoutChoiceAction(defaultEmbedding));
}
@@ -122,21 +123,22 @@ const doInitialDataLoad = () =>
}
}, true);
function requestSingleGeneExpressionCountsForColoringPOST(gene) {
function requestSingleGeneExpressionCountsForColoringPOST(gene: any) {
return {
type: "color by expression",
gene,
};
}
const requestUserDefinedGene = (gene) => ({
const requestUserDefinedGene = (gene: any) => ({
type: "request user defined gene success",
data: {
genes: [gene],
},
});
const dispatchDiffExpErrors = (dispatch, response) => {
const dispatchDiffExpErrors = (dispatch: any, response: any) => {
switch (response.status) {
case 403:
dispatchNetworkErrorMessageToUser(
@@ -159,10 +161,11 @@ const dispatchDiffExpErrors = (dispatch, response) => {
}
};
const requestDifferentialExpression = (set1, set2, num_genes = 50) => async (
dispatch,
getState
) => {
const requestDifferentialExpression = (
set1: any,
set2: any,
num_genes = 50
) => async (dispatch: any, getState: any) => {
dispatch({ type: "request differential expression started" });
try {
/*
@@ -210,7 +213,8 @@ const requestDifferentialExpression = (set1, set2, num_genes = 50) => async (
const varIndex = await annoMatrix.fetch("var", varIndexName);
const diffexpLists = { negative: [], positive: [] };
for (const polarity of Object.keys(diffexpLists)) {
diffexpLists[polarity] = response[polarity].map((v) => [
// @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message
diffexpLists[polarity] = response[polarity].map((v: any) => [
varIndex.at(v[0], varIndexName),
...v.slice(1),
]);
@@ -229,7 +233,7 @@ const requestDifferentialExpression = (set1, set2, num_genes = 50) => async (
}
};
function fetchJson(pathAndQuery) {
function fetchJson(pathAndQuery: any) {
return doJsonRequest(
`${globals.API.prefix}${globals.API.version}${pathAndQuery}`
);
client/src/actions/selection.js → client/src/actions/selection.ts
+39 -32
View File
@@ -2,11 +2,11 @@
Action creators for selection
*/
export const selectContinuousMetadataAction = (
type,
query,
range,
type: any,
query: any,
range: any,
oldProps = {}
) => async (dispatch, getState) => {
) => async (dispatch: any, getState: any) => {
const { obsCrossfilter: prevObsCrossfilter } = getState();
const selection = range
@@ -29,13 +29,13 @@ export const selectContinuousMetadataAction = (
};
export const selectCategoricalMetadataAction = (
type, // action type
metadataField, // annotation category name
labels,
label, // the label being selected/deselected
isSelected, // bool
type: any, // action type
metadataField: any, // annotation category name
labels: any,
label: any, // the label being selected/deselected
isSelected: any, // bool
oldProps = {}
) => async (dispatch, getState) => {
) => async (dispatch: any, getState: any) => {
const {
obsCrossfilter: prevObsCrossfilter,
categoricalSelection,
@@ -43,7 +43,7 @@ export const selectCategoricalMetadataAction = (
const labelSelectionState = new Map(categoricalSelection[metadataField]);
labels.forEach(
(l) => labelSelectionState.has(l) || labelSelectionState.set(l, true)
(l: any) => labelSelectionState.has(l) || labelSelectionState.set(l, true)
);
labelSelectionState.set(label, isSelected);
@@ -70,19 +70,19 @@ export const selectCategoricalMetadataAction = (
};
export const selectCategoricalAllMetadataAction = (
type, // action type
metadataField, // annotation category name
labels,
isSelected, // bool, select all or none
type: any, // action type
metadataField: any, // annotation category name
labels: any,
isSelected: any, // bool, select all or none
oldProps = {}
) => async (dispatch, getState) => {
) => async (dispatch: any, getState: any) => {
const {
obsCrossfilter: prevObsCrossfilter,
categoricalSelection,
} = getState();
const labelSelectionState = new Map(categoricalSelection[metadataField]);
labels.forEach((label) => labelSelectionState.set(label, isSelected));
labels.forEach((label: any) => labelSelectionState.set(label, isSelected));
const selection = { mode: isSelected ? "all" : "none" };
const obsCrossfilter = await prevObsCrossfilter.select(
@@ -108,10 +108,11 @@ export const graphBrushStartAction = () =>
/* no change to crossfilter until a change fires */
({ type: "graph brush start" });
const _graphBrushWithinRectAction = (type, embName, brushCoords) => async (
dispatch,
getState
) => {
const _graphBrushWithinRectAction = (
type: any,
embName: any,
brushCoords: any
) => async (dispatch: any, getState: any) => {
const { obsCrossfilter: prevObsCrossfilter } = getState();
const selection = { mode: "within-rect", ...brushCoords };
@@ -128,7 +129,10 @@ const _graphBrushWithinRectAction = (type, embName, brushCoords) => async (
});
};
const _graphAllAction = (type, embName) => async (dispatch, getState) => {
const _graphAllAction = (type: any, embName: any) => async (
dispatch: any,
getState: any
) => {
const { obsCrossfilter: prevObsCrossfilter } = getState();
const obsCrossfilter = await prevObsCrossfilter.select("emb", embName, {
@@ -141,30 +145,30 @@ const _graphAllAction = (type, embName) => async (dispatch, getState) => {
});
};
export const graphBrushChangeAction = (embName, brushCoords) =>
export const graphBrushChangeAction = (embName: any, brushCoords: any) =>
_graphBrushWithinRectAction("graph brush change", embName, brushCoords);
export const graphBrushEndAction = (embName, brushCoords) =>
export const graphBrushEndAction = (embName: any, brushCoords: any) =>
_graphBrushWithinRectAction("graph brush end", embName, brushCoords);
export const graphBrushCancelAction = (embName) =>
export const graphBrushCancelAction = (embName: any) =>
_graphAllAction("graph brush cancel", embName);
export const graphBrushDeselectAction = (embName) =>
export const graphBrushDeselectAction = (embName: any) =>
_graphAllAction("graph brush deselect", embName);
export const graphLassoStartAction = () =>
/* no change to crossfilter until a change fires */
({ type: "graph lasso start" });
export const graphLassoCancelAction = (embName) =>
export const graphLassoCancelAction = (embName: any) =>
_graphAllAction("graph lasso cancel", embName);
export const graphLassoDeselectAction = (embName) =>
export const graphLassoDeselectAction = (embName: any) =>
_graphAllAction("graph lasso cancel", embName);
export const graphLassoEndAction = (embName, polygon) => async (
dispatch,
getState
export const graphLassoEndAction = (embName: any, polygon: any) => async (
dispatch: any,
getState: any
) => {
const { obsCrossfilter: prevObsCrossfilter } = getState();
@@ -188,7 +192,10 @@ export const graphLassoEndAction = (embName, polygon) => async (
/*
Differential expression set selection
*/
export const setCellSetFromSelection = (cellSetId) => (dispatch, getState) => {
export const setCellSetFromSelection = (cellSetId: any) => (
dispatch: any,
getState: any
) => {
const { obsCrossfilter } = getState();
const selected = obsCrossfilter.allSelectedLabels();
client/src/actions/viewStack.js → client/src/actions/viewStack.ts
+6 -3
View File
@@ -18,7 +18,10 @@ import {
_userResetSubsetAnnoMatrix,
} from "../util/stateManager/viewStackHelpers";
export const clipAction = (min, max) => (dispatch, getState) => {
export const clipAction = (min: any, max: any) => (
dispatch: any,
getState: any
) => {
/*
apply a clip to the current annoMatrix. By convention, the clip
view is ALWAYS the top view.
@@ -34,7 +37,7 @@ export const clipAction = (min, max) => (dispatch, getState) => {
});
};
export const subsetAction = () => (dispatch, getState) => {
export const subsetAction = () => (dispatch: any, getState: any) => {
/*
Subset the annoMatrix to the current crossfilter selection by pushing a
subset view.
@@ -58,7 +61,7 @@ export const subsetAction = () => (dispatch, getState) => {
});
};
export const resetSubsetAction = () => (dispatch, getState) => {
export const resetSubsetAction = () => (dispatch: any, getState: any) => {
/*
Reset the annoMatrix to all data. Because we may have multiple views
stacked, we pop them all. By convention, any clip transformation will
client/src/annoMatrix/annoMatrix.js → client/src/annoMatrix/annoMatrix.ts
+69 -13
View File
@@ -17,6 +17,28 @@ import { _queryValidate, _queryCacheKey } from "./query";
const _dataframeCache = dataframeMemo(128);
export default class AnnoMatrix {
public isView: any;
public nObs: any;
public nVar: any;
public rowIndex: any;
public schema: any;
public userFlags: any;
public viewOf: any;
protected _cache: any;
private _pendingLoad: any;
private _whereCache: any;
private _gcInfo: any;
/*
Abstract base class for all AnnoMatrix objects. This class provides a proxy
to the annotated matrix data authoritatively served by the server/back-end.
@@ -54,7 +76,7 @@ export default class AnnoMatrix {
return ["obs", "var", "emb", "X"];
}
constructor(schema, nObs, nVar, rowIndex = null) {
constructor(schema: any, nObs: any, nVar: any, rowIndex = null) {
/*
Private constructor - this is an abstract base class. Do not use.
*/
@@ -109,6 +131,7 @@ export default class AnnoMatrix {
/**
** Schema helper/accessors
**/
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
getMatrixColumns(field) {
/*
Return array of column names in the field. ONLY supported on the
@@ -132,6 +155,7 @@ export default class AnnoMatrix {
return AnnoMatrix.fields();
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
getColumnSchema(field, col) {
/*
Return the schema for the field & column ,eg,
@@ -144,6 +168,7 @@ export default class AnnoMatrix {
return _getColumnSchema(this.schema, field, col);
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
getColumnDimensions(field, col) {
/*
Return the dimensions on this field / column. For most fields, which are 1D,
@@ -174,6 +199,7 @@ export default class AnnoMatrix {
/**
** Load / read interfaces
**/
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
fetch(field, q) {
/*
Return the given query on a single matrix field as a single dataframe.
@@ -231,6 +257,7 @@ export default class AnnoMatrix {
return this._fetch(field, q);
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
prefetch(field, q) {
/*
Start a data fetch & cache fill. Identical to fetch() except it does
@@ -261,7 +288,8 @@ export default class AnnoMatrix {
** The actual implementation is in the sub-classes, which MUST override these.
**/
// eslint-disable-next-line class-methods-use-this, no-unused-vars -- make sure subclass implements
// @ts-expect-error ts-migrate(6133) FIXME: 'col' is declared but its value is never read.
// eslint-disable-next-line class-methods-use-this, @typescript-eslint/no-unused-vars -- make sure subclass implements
addObsAnnoCategory(col, category) {
/*
Add a new category value (aka "label") to a writable obs column, and return the new AnnoMatrix.
@@ -278,7 +306,8 @@ export default class AnnoMatrix {
_subclassResponsibility();
}
// eslint-disable-next-line class-methods-use-this, no-unused-vars -- make sure subclass implements
// @ts-expect-error ts-migrate(6133) FIXME: 'col' is declared but its value is never read.
// eslint-disable-next-line class-methods-use-this, @typescript-eslint/no-unused-vars -- make sure subclass implements
async removeObsAnnoCategory(col, category, unassignedCategory) {
/*
Remove a category value from an obs column, reassign any obs having that value
@@ -299,7 +328,8 @@ export default class AnnoMatrix {
_subclassResponsibility();
}
// eslint-disable-next-line class-methods-use-this, no-unused-vars -- make sure subclass implements
// @ts-expect-error ts-migrate(6133) FIXME: 'col' is declared but its value is never read.
// eslint-disable-next-line class-methods-use-this, @typescript-eslint/no-unused-vars -- make sure subclass implements
dropObsColumn(col) {
/*
Drop an entire writable column, eg a user-created obs annotation. Typical use
@@ -315,7 +345,8 @@ export default class AnnoMatrix {
_subclassResponsibility();
}
// eslint-disable-next-line class-methods-use-this, no-unused-vars -- make sure subclass implements
// @ts-expect-error ts-migrate(6133) FIXME: 'colSchema' is declared but its value is never rea... Remove this comment to see the full error message
// eslint-disable-next-line class-methods-use-this, @typescript-eslint/no-unused-vars -- make sure subclass implements
addObsColumn(colSchema, Ctor, value) {
/*
Add a new writable OBS annotation column, with the caller-specified schema, initial value
@@ -344,7 +375,8 @@ export default class AnnoMatrix {
_subclassResponsibility();
}
// eslint-disable-next-line class-methods-use-this, no-unused-vars -- make sure subclass implements
// @ts-expect-error ts-migrate(6133) FIXME: 'oldCol' is declared but its value is never read.
// eslint-disable-next-line class-methods-use-this, @typescript-eslint/no-unused-vars -- make sure subclass implements
renameObsColumn(oldCol, newCol) {
/*
Rename the obs column 'oldCol' to have name 'newCol' and returns new AnnoMatrix.
@@ -359,7 +391,8 @@ export default class AnnoMatrix {
_subclassResponsibility();
}
// eslint-disable-next-line class-methods-use-this, no-unused-vars -- make sure subclass implements
// @ts-expect-error ts-migrate(6133) FIXME: 'col' is declared but its value is never read.
// eslint-disable-next-line class-methods-use-this, @typescript-eslint/no-unused-vars -- make sure subclass implements
async setObsColumnValues(col, obsLabels, value) {
/*
Set all obs with label in array 'obsLabels' to have 'value'. Typical use would be
@@ -377,7 +410,8 @@ export default class AnnoMatrix {
_subclassResponsibility();
}
// eslint-disable-next-line class-methods-use-this, no-unused-vars -- make sure subclass implements
// @ts-expect-error ts-migrate(6133) FIXME: 'col' is declared but its value is never read.
// eslint-disable-next-line class-methods-use-this, @typescript-eslint/no-unused-vars -- make sure subclass implements
async resetObsColumnValues(col, oldValue, newValue) {
/*
Set by value - all elements in the column with value 'oldValue' are set to 'newValue'.
@@ -394,7 +428,8 @@ export default class AnnoMatrix {
_subclassResponsibility();
}
// eslint-disable-next-line class-methods-use-this, no-unused-vars -- make sure subclass implements
// @ts-expect-error ts-migrate(6133) FIXME: 'colSchema' is declared but its value is never rea... Remove this comment to see the full error message
// eslint-disable-next-line class-methods-use-this, @typescript-eslint/no-unused-vars -- make sure subclass implements
addEmbedding(colSchema) {
/*
Add a new obs embedding to the AnnoMatrix, with provided schema.
@@ -407,6 +442,7 @@ export default class AnnoMatrix {
_subclassResponsibility();
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
getCacheKeys(field, query) {
/*
Return cache keys for columns associated with this query. May return
@@ -418,17 +454,23 @@ export default class AnnoMatrix {
/**
** Private interfaces below.
**/
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
_resolveCachedQueries(field, queries) {
return queries
return (
queries
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'query' implicitly has an 'any' type.
.map((query) =>
_whereCacheGet(this._whereCache, this.schema, field, query).filter(
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'cacheKey' implicitly has an 'any' type.
(cacheKey) =>
cacheKey !== undefined && this._cache[field].hasCol(cacheKey)
)
)
.flat();
.flat()
);
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
async _fetch(field, q) {
if (!AnnoMatrix.fields().includes(field)) return undefined;
const queries = Array.isArray(q) ? q : [q];
@@ -441,6 +483,7 @@ export default class AnnoMatrix {
/* find any query not already cached */
const uncachedQueries = queries.filter((query) =>
_whereCacheGet(this._whereCache, this.schema, field, query).some(
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'cacheKey' implicitly has an 'any' type.
(cacheKey) =>
cacheKey === undefined || !this._cache[field].hasCol(cacheKey)
)
@@ -450,8 +493,10 @@ export default class AnnoMatrix {
if (uncachedQueries.length > 0) {
await Promise.all(
uncachedQueries.map((query) =>
// @ts-expect-error ts-migrate(7006) FIXME: Parameter '_field' implicitly has an 'any' type.
this._getPendingLoad(field, query, async (_field, _query) => {
/* fetch, then index. _doLoad is subclass interface */
// @ts-expect-error ts-migrate(2488) FIXME: Type 'void' must have a '[Symbol.iterator]()' meth... Remove this comment to see the full error message
const [whereCacheUpdate, df] = await this._doLoad(_field, _query);
this._cache[_field] = this._cache[_field].withColsFrom(df);
this._whereCache = _whereCacheMerge(
@@ -472,6 +517,7 @@ export default class AnnoMatrix {
return response;
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
async _getPendingLoad(field, query, fetchFn) {
/*
Given a query on a field, ensure that we only have a single outstanding
@@ -527,19 +573,21 @@ export default class AnnoMatrix {
To be effective, the GC callback needs to be invoked from the undo/redo code,
as much of the cache is pinned by that data structure.
*/
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
_gcField(field, isHot, pinnedColumns) {
const maxColumns = isHot ? 256 : 10; // maybe to aggressive?
const maxColumns = isHot ? 256 : 10;
const cache = this._cache[field];
if (cache.colIndex.size() < maxColumns) return; // trivial rejection
const candidates = cache.colIndex
.labels()
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'col' implicitly has an 'any' type.
.filter((col) => !pinnedColumns.includes(col));
const excessCount = candidates.length + pinnedColumns.length - maxColumns;
if (excessCount > 0) {
const { _gcInfo } = this;
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'a' implicitly has an 'any' type.
candidates.sort((a, b) => {
let atime = _gcInfo.get(_columnCacheKey(field, a));
if (atime === undefined) atime = 0;
@@ -558,13 +606,16 @@ export default class AnnoMatrix {
// )}]`
// );
this._cache[field] = toDrop.reduce(
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'df' implicitly has an 'any' type.
(df, col) => df.dropCol(col),
this._cache[field]
);
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'col' implicitly has an 'any' type.
toDrop.forEach((col) => _gcInfo.delete(_columnCacheKey(field, col)));
}
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
_gcFetchCleanup(field, pinnedColumns) {
/*
Called during data load/fetch. By definition, this is 'hot', so we
@@ -579,6 +630,7 @@ export default class AnnoMatrix {
}
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'hints' implicitly has an 'any' type.
_gc(hints) {
/*
Called from middleware, or elsewhere. isHot is true if we are in the active store,
@@ -591,6 +643,7 @@ export default class AnnoMatrix {
);
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
_gcUpdateStats(field, dataframe) {
/*
called each time a query is performed, allowing the gc to update any bookkeeping
@@ -600,6 +653,7 @@ export default class AnnoMatrix {
const cols = dataframe.colIndex.labels();
const { _gcInfo } = this;
const now = Date.now();
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'c' implicitly has an 'any' type.
cols.forEach((c) => {
_gcInfo.set(_columnCacheKey(field, c), now);
});
@@ -617,6 +671,7 @@ export default class AnnoMatrix {
Do not override _clone();
**/
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'clone' implicitly has an 'any' type.
_cloneDeeper(clone) {
clone._cache = _shallowClone(this._cache);
clone._gcInfo = new Map();
@@ -640,6 +695,7 @@ export default class AnnoMatrix {
/*
private utility functions below
*/
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
function _columnCacheKey(field, column) {
return `${field}/${column}`;
}
client/src/annoMatrix/clone.js → client/src/annoMatrix/clone.ts
+1 -1
View File
@@ -1,6 +1,6 @@
/*
Shallow clone an object, correctly handling prototype
*/
export default function _shallowClone(orig) {
export default function _shallowClone(orig: any) {
return Object.assign(Object.create(Object.getPrototypeOf(orig)), orig);
}
client/src/annoMatrix/crossfilter.js → client/src/annoMatrix/crossfilter.ts
+81 -31
View File
@@ -10,26 +10,31 @@ AnnoMatrix stay in sync:
import Crossfilter from "../util/typedCrossfilter";
import { _getColumnSchema } from "./schema";
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
function _dimensionNameFromDf(field, df) {
const colNames = df.colIndex.labels();
return _dimensionName(field, colNames);
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
function _dimensionName(field, colNames) {
if (!Array.isArray(colNames)) return `${field}/${colNames}`;
return `${field}/${colNames.join(":")}`;
}
export default class AnnoMatrixObsCrossfilter {
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'annoMatrix' implicitly has an 'any' typ... Remove this comment to see the full error message
constructor(annoMatrix, _obsCrossfilter = null) {
this.annoMatrix = annoMatrix;
this.obsCrossfilter =
(this as any).annoMatrix = annoMatrix;
(this as any).obsCrossfilter =
_obsCrossfilter || new Crossfilter(annoMatrix._cache.obs);
this.obsCrossfilter = this.obsCrossfilter.setData(annoMatrix._cache.obs);
(this as any).obsCrossfilter = (this as any).obsCrossfilter.setData(
annoMatrix._cache.obs
);
}
size() {
return this.obsCrossfilter.size();
return (this as any).obsCrossfilter.size();
}
/**
@@ -39,14 +44,23 @@ export default class AnnoMatrixObsCrossfilter {
See API documentation in annoMatrix.js.
**/
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'colSchema' implicitly has an 'any' type... Remove this comment to see the full error message
addObsColumn(colSchema, Ctor, value) {
const annoMatrix = this.annoMatrix.addObsColumn(colSchema, Ctor, value);
const obsCrossfilter = this.obsCrossfilter.setData(annoMatrix._cache.obs);
const annoMatrix = (this as any).annoMatrix.addObsColumn(
colSchema,
Ctor,
value
);
const obsCrossfilter = (this as any).obsCrossfilter.setData(
annoMatrix._cache.obs
);
return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter);
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'col' implicitly has an 'any' type.
dropObsColumn(col) {
const annoMatrix = this.annoMatrix.dropObsColumn(col);
const annoMatrix = (this as any).annoMatrix.dropObsColumn(col);
// @ts-expect-error ts-migrate(2339) FIXME: Property 'obsCrossfilter' does not exist on type '... Remove this comment to see the full error message
let { obsCrossfilter } = this;
const dimName = _dimensionName("obs", col);
if (obsCrossfilter.hasDimension(dimName)) {
@@ -55,10 +69,12 @@ export default class AnnoMatrixObsCrossfilter {
return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter);
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'oldCol' implicitly has an 'any' type.
renameObsColumn(oldCol, newCol) {
const annoMatrix = this.annoMatrix.renameObsColumn(oldCol, newCol);
const annoMatrix = (this as any).annoMatrix.renameObsColumn(oldCol, newCol);
const oldDimName = _dimensionName("obs", oldCol);
const newDimName = _dimensionName("obs", newCol);
// @ts-expect-error ts-migrate(2339) FIXME: Property 'obsCrossfilter' does not exist on type '... Remove this comment to see the full error message
let { obsCrossfilter } = this;
if (obsCrossfilter.hasDimension(oldDimName)) {
obsCrossfilter = obsCrossfilter.renameDimension(oldDimName, newDimName);
@@ -66,9 +82,14 @@ export default class AnnoMatrixObsCrossfilter {
return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter);
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'col' implicitly has an 'any' type.
addObsAnnoCategory(col, category) {
const annoMatrix = this.annoMatrix.addObsAnnoCategory(col, category);
const annoMatrix = (this as any).annoMatrix.addObsAnnoCategory(
col,
category
);
const dimName = _dimensionName("obs", col);
// @ts-expect-error ts-migrate(2339) FIXME: Property 'obsCrossfilter' does not exist on type '... Remove this comment to see the full error message
let { obsCrossfilter } = this;
if (obsCrossfilter.hasDimension(dimName)) {
obsCrossfilter = obsCrossfilter.delDimension(dimName);
@@ -76,13 +97,15 @@ export default class AnnoMatrixObsCrossfilter {
return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter);
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'col' implicitly has an 'any' type.
async removeObsAnnoCategory(col, category, unassignedCategory) {
const annoMatrix = await this.annoMatrix.removeObsAnnoCategory(
const annoMatrix = await (this as any).annoMatrix.removeObsAnnoCategory(
col,
category,
unassignedCategory
);
const dimName = _dimensionName("obs", col);
// @ts-expect-error ts-migrate(2339) FIXME: Property 'obsCrossfilter' does not exist on type '... Remove this comment to see the full error message
let { obsCrossfilter } = this;
if (obsCrossfilter.hasDimension(dimName)) {
obsCrossfilter = obsCrossfilter.delDimension(dimName);
@@ -90,13 +113,15 @@ export default class AnnoMatrixObsCrossfilter {
return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter);
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'col' implicitly has an 'any' type.
async setObsColumnValues(col, rowLabels, value) {
const annoMatrix = await this.annoMatrix.setObsColumnValues(
const annoMatrix = await (this as any).annoMatrix.setObsColumnValues(
col,
rowLabels,
value
);
const dimName = _dimensionName("obs", col);
// @ts-expect-error ts-migrate(2339) FIXME: Property 'obsCrossfilter' does not exist on type '... Remove this comment to see the full error message
let { obsCrossfilter } = this;
if (obsCrossfilter.hasDimension(dimName)) {
obsCrossfilter = obsCrossfilter.delDimension(dimName);
@@ -104,13 +129,15 @@ export default class AnnoMatrixObsCrossfilter {
return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter);
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'col' implicitly has an 'any' type.
async resetObsColumnValues(col, oldValue, newValue) {
const annoMatrix = await this.annoMatrix.resetObsColumnValues(
const annoMatrix = await (this as any).annoMatrix.resetObsColumnValues(
col,
oldValue,
newValue
);
const dimName = _dimensionName("obs", col);
// @ts-expect-error ts-migrate(2339) FIXME: Property 'obsCrossfilter' does not exist on type '... Remove this comment to see the full error message
let { obsCrossfilter } = this;
if (obsCrossfilter.hasDimension(dimName)) {
obsCrossfilter = obsCrossfilter.delDimension(dimName);
@@ -118,9 +145,13 @@ export default class AnnoMatrixObsCrossfilter {
return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter);
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'colSchema' implicitly has an 'any' type... Remove this comment to see the full error message
addEmbedding(colSchema) {
const annoMatrix = this.annoMatrix.addEmbedding(colSchema);
return new AnnoMatrixObsCrossfilter(annoMatrix, this.obsCrossfilter);
const annoMatrix = (this as any).annoMatrix.addEmbedding(colSchema);
return new AnnoMatrixObsCrossfilter(
annoMatrix,
(this as any).obsCrossfilter
);
}
/**
@@ -128,11 +159,15 @@ export default class AnnoMatrixObsCrossfilter {
* want to stop trackin the selection state, but aren't sure we want to blow the
* annomatrix cache.
*/
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
dropDimension(field, query) {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'annoMatrix' does not exist on type 'Anno... Remove this comment to see the full error message
const { annoMatrix } = this;
// @ts-expect-error ts-migrate(2339) FIXME: Property 'obsCrossfilter' does not exist on type '... Remove this comment to see the full error message
let { obsCrossfilter } = this;
const keys = annoMatrix
.getCacheKeys(field, query)
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'k' implicitly has an 'any' type.
.filter((k) => k !== undefined);
const dimName = _dimensionName(field, keys);
if (obsCrossfilter.hasDimension(dimName)) {
@@ -146,8 +181,11 @@ export default class AnnoMatrixObsCrossfilter {
are just wrappers to lazy create indices.
**/
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
async select(field, query, spec) {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'annoMatrix' does not exist on type 'Anno... Remove this comment to see the full error message
const { annoMatrix } = this;
// @ts-expect-error ts-migrate(2339) FIXME: Property 'obsCrossfilter' does not exist on type '... Remove this comment to see the full error message
let { obsCrossfilter } = this;
if (!annoMatrix?._cache?.[field]) {
@@ -180,55 +218,59 @@ export default class AnnoMatrixObsCrossfilter {
/*
Select all on any dimension in this field.
*/
// @ts-expect-error ts-migrate(2339) FIXME: Property 'annoMatrix' does not exist on type 'Anno... Remove this comment to see the full error message
const { annoMatrix } = this;
const currentDims = this.obsCrossfilter.dimensionNames();
const currentDims = (this as any).obsCrossfilter.dimensionNames();
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'xfltr' implicitly has an 'any' type.
const obsCrossfilter = currentDims.reduce((xfltr, dim) => {
return xfltr.select(dim, { mode: "all" });
}, this.obsCrossfilter);
}, (this as any).obsCrossfilter);
return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter);
}
countSelected() {
/* if no data yet indexed in the crossfilter, just say everything is selected */
if (this.obsCrossfilter.size() === 0) return this.annoMatrix.nObs;
return this.obsCrossfilter.countSelected();
if ((this as any).obsCrossfilter.size() === 0)
return (this as any).annoMatrix.nObs;
return (this as any).obsCrossfilter.countSelected();
}
allSelectedMask() {
/* if no data yet indexed in the crossfilter, just say everything is selected */
if (
this.obsCrossfilter.size() === 0 ||
this.obsCrossfilter.dimensionNames().length === 0
(this as any).obsCrossfilter.size() === 0 ||
(this as any).obsCrossfilter.dimensionNames().length === 0
) {
/* fake the mask */
return new Uint8Array(this.annoMatrix.nObs).fill(1);
return new Uint8Array((this as any).annoMatrix.nObs).fill(1);
}
return this.obsCrossfilter.allSelectedMask();
return (this as any).obsCrossfilter.allSelectedMask();
}
allSelectedLabels() {
/* if no data yet indexed in the crossfilter, just say everything is selected */
if (
this.obsCrossfilter.size() === 0 ||
this.obsCrossfilter.dimensionNames().length === 0
(this as any).obsCrossfilter.size() === 0 ||
(this as any).obsCrossfilter.dimensionNames().length === 0
) {
return this.annoMatrix.rowIndex.labels();
return (this as any).annoMatrix.rowIndex.labels();
}
const mask = this.obsCrossfilter.allSelectedMask();
const index = this.annoMatrix.rowIndex.isubsetMask(mask);
const mask = (this as any).obsCrossfilter.allSelectedMask();
const index = (this as any).annoMatrix.rowIndex.isubsetMask(mask);
return index.labels();
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'array' implicitly has an 'any' type.
fillByIsSelected(array, selectedValue, deselectedValue) {
/* if no data yet indexed in the crossfilter, just say everything is selected */
if (
this.obsCrossfilter.size() === 0 ||
this.obsCrossfilter.dimensionNames().length === 0
(this as any).obsCrossfilter.size() === 0 ||
(this as any).obsCrossfilter.dimensionNames().length === 0
) {
return array.fill(selectedValue);
}
return this.obsCrossfilter.fillByIsSelected(
return (this as any).obsCrossfilter.fillByIsSelected(
array,
selectedValue,
deselectedValue
@@ -239,21 +281,29 @@ export default class AnnoMatrixObsCrossfilter {
** Private below
**/
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'annoMatrix' implicitly has an 'any' typ... Remove this comment to see the full error message
_addObsCrossfilterDimension(annoMatrix, obsCrossfilter, field, df) {
if (field === "var") return obsCrossfilter;
const dimName = _dimensionNameFromDf(field, df);
const dimParams = this._getObsDimensionParams(field, df);
obsCrossfilter = obsCrossfilter.setData(annoMatrix._cache.obs);
// @ts-expect-error ts-migrate(2488) FIXME: Type 'any[] | undefined' must have a '[Symbol.iter... Remove this comment to see the full error message
obsCrossfilter = obsCrossfilter.addDimension(dimName, ...dimParams);
return obsCrossfilter;
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
_getColumnBaseType(field, col) {
/* Look up the primitive type for this field/col */
const colSchema = _getColumnSchema(this.annoMatrix.schema, field, col);
const colSchema = _getColumnSchema(
(this as any).annoMatrix.schema,
field,
col
);
return colSchema.type;
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
_getObsDimensionParams(field, df) {
/* return the crossfilter dimensiontype type and params for this field/dataframe */
client/src/annoMatrix/fetchHelpers.js → client/src/annoMatrix/fetchHelpers.ts
+4 -4
View File
@@ -1,19 +1,19 @@
export { doBinaryRequest, doFetch } from "../util/actionHelpers";
/* double URI encode - needed for query-param filters */
export function _dubEncURIComp(s) {
export function _dubEncURIComp(s: any) {
return encodeURIComponent(encodeURIComponent(s));
}
/* currently unused, consider deleting */
export function _fetchResult(promise) {
export function _fetchResult(promise: any) {
let _status = "pending";
const res = promise.then(
(r) => {
(r: any) => {
_status = "success";
return r;
},
(e) => {
(e: any) => {
_status = "error";
throw e;
}
client/src/annoMatrix/index.js → client/src/annoMatrix/index.ts
View File
client/src/annoMatrix/loader.js → client/src/annoMatrix/loader.ts
+39 -17
View File
@@ -23,6 +23,8 @@ import {
const promiseThrottle = new PromiseLimit(5);
export default class AnnoMatrixLoader extends AnnoMatrix {
baseURL: any;
/*
AnnoMatrix implementation which proxies to HTTP server using the CXG REST API.
Used as the base (non-view) instance.
@@ -33,7 +35,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
new AnnoMatrixLoader(serverBaseURL, schema) -> instance
*/
constructor(baseURL, schema) {
constructor(baseURL: any, schema: any) {
const { nObs, nVar } = schema.dataframe;
super(schema, nObs, nVar);
@@ -48,7 +50,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
/**
** Public. API described in base class.
**/
addObsAnnoCategory(col, category) {
addObsAnnoCategory(col: any, category: any) {
/*
Add a new category (aka label) to the schema for an obs column.
*/
@@ -60,7 +62,11 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
return newAnnoMatrix;
}
async removeObsAnnoCategory(col, category, unassignedCategory) {
async removeObsAnnoCategory(
col: any,
category: any,
unassignedCategory: any
) {
/*
Remove a single "category" (aka "label") from the data & schema of an obs column.
*/
@@ -80,7 +86,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
return newAnnoMatrix;
}
dropObsColumn(col) {
dropObsColumn(col: any) {
/*
drop column from field
*/
@@ -88,11 +94,12 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
_writableCheck(colSchema); // throws on error
const newAnnoMatrix = this._clone();
newAnnoMatrix._cache.obs = this._cache.obs.dropCol(col);
newAnnoMatrix._cache.obs = (this as any)._cache.obs.dropCol(col);
newAnnoMatrix.schema = removeObsAnnoColumn(this.schema, col);
return newAnnoMatrix;
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'colSchema' implicitly has an 'any' type... Remove this comment to see the full error message
addObsColumn(colSchema, Ctor, value) {
/*
add a column to field, initializing with value. Value may
@@ -105,7 +112,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
const colName = colSchema.name;
if (
_getColumnSchema(this.schema, "obs", colName) ||
this._cache.obs.hasCol(colName)
(this as any)._cache.obs.hasCol(colName)
) {
throw new Error("column already exists");
}
@@ -121,7 +128,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
} else {
data = new Ctor(this.nObs).fill(value);
}
newAnnoMatrix._cache.obs = this._cache.obs.withCol(colName, data);
newAnnoMatrix._cache.obs = (this as any)._cache.obs.withCol(colName, data);
_normalizeCategoricalSchema(
colSchema,
newAnnoMatrix._cache.obs.col(colName)
@@ -130,15 +137,15 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
return newAnnoMatrix;
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'oldCol' implicitly has an 'any' type.
renameObsColumn(oldCol, newCol) {
/*
Rename the obs oldColName to newColName. oldCol must be writable.
*/
const oldColSchema = _getColumnSchema(this.schema, "obs", oldCol);
_writableCheck(oldColSchema); // throws on error
const value = this._cache.obs.hasCol(oldCol)
? this._cache.obs.col(oldCol).asArray()
_writableCheck(oldColSchema);
const value = (this as any)._cache.obs.hasCol(oldCol)
? (this as any)._cache.obs.col(oldCol).asArray()
: undefined;
return this.dropObsColumn(oldCol).addObsColumn(
{
@@ -150,6 +157,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
);
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'col' implicitly has an 'any' type.
async setObsColumnValues(col, rowLabels, value) {
/*
Set all rows identified by rowLabels to value.
@@ -159,11 +167,11 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
// ensure that we have the data in cache before we manipulate it
await this.fetch("obs", col);
if (!this._cache.obs.hasCol(col))
if (!(this as any)._cache.obs.hasCol(col))
throw new Error("Internal error - user annotation data missing");
const rowIndices = this.rowIndex.getOffsets(rowLabels);
const data = this._cache.obs.col(col).asArray().slice();
const data = (this as any)._cache.obs.col(col).asArray().slice();
for (let i = 0, len = rowIndices.length; i < len; i += 1) {
const idx = rowIndices[i];
if (idx === undefined) throw new Error("Unknown row label");
@@ -171,7 +179,10 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
}
const newAnnoMatrix = this._clone();
newAnnoMatrix._cache.obs = this._cache.obs.replaceColData(col, data);
newAnnoMatrix._cache.obs = (this as any)._cache.obs.replaceColData(
col,
data
);
const { categories } = colSchema;
if (!categories?.includes(value)) {
newAnnoMatrix.schema = addObsAnnoCategory(this.schema, col, value);
@@ -179,6 +190,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
return newAnnoMatrix;
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'col' implicitly has an 'any' type.
async resetObsColumnValues(col, oldValue, newValue) {
/*
Set all rows with value 'oldValue' to 'newValue'.
@@ -192,16 +204,19 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
// ensure that we have the data in cache before we manipulate it
await this.fetch("obs", col);
if (!this._cache.obs.hasCol(col))
if (!(this as any)._cache.obs.hasCol(col))
throw new Error("Internal error - user annotation data missing");
const data = this._cache.obs.col(col).asArray().slice();
const data = (this as any)._cache.obs.col(col).asArray().slice();
for (let i = 0, l = data.length; i < l; i += 1) {
if (data[i] === oldValue) data[i] = newValue;
}
const newAnnoMatrix = this._clone();
newAnnoMatrix._cache.obs = this._cache.obs.replaceColData(col, data);
newAnnoMatrix._cache.obs = (this as any)._cache.obs.replaceColData(
col,
data
);
const { categories } = colSchema;
if (!categories?.includes(newValue)) {
newAnnoMatrix.schema = addObsAnnoCategory(this.schema, col, newValue);
@@ -209,6 +224,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
return newAnnoMatrix;
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'colSchema' implicitly has an 'any' type... Remove this comment to see the full error message
addEmbedding(colSchema) {
/*
add new layout to the obs embeddings
@@ -226,6 +242,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
/**
** Private below
**/
// @ts-expect-error ts-migrate(2416) FIXME: Property '_doLoad' in type 'AnnoMatrixLoader' is n... Remove this comment to see the full error message
async _doLoad(field, query) {
/*
_doLoad - evaluates the query against the field. Returns:
@@ -280,12 +297,14 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
Utility functions below
*/
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'colSchema' implicitly has an 'any' type... Remove this comment to see the full error message
function _writableCheck(colSchema) {
if (!colSchema?.writable) {
throw new Error("Unknown or readonly obs column");
}
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'colSchema' implicitly has an 'any' type... Remove this comment to see the full error message
function _writableCategoryTypeCheck(colSchema) {
_writableCheck(colSchema);
if (colSchema.type !== "categorical") {
@@ -293,6 +312,7 @@ function _writableCategoryTypeCheck(colSchema) {
}
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'baseURL' implicitly has an 'any' type.
function _embLoader(baseURL, _field, query) {
_expectSimpleQuery(query);
@@ -302,6 +322,7 @@ function _embLoader(baseURL, _field, query) {
return () => doBinaryRequest(url);
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'baseURL' implicitly has an 'any' type.
function _obsOrVarLoader(baseURL, field, query) {
_expectSimpleQuery(query);
@@ -311,6 +332,7 @@ function _obsOrVarLoader(baseURL, field, query) {
return () => doBinaryRequest(url);
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'baseURL' implicitly has an 'any' type.
function _XLoader(baseURL, field, query) {
_expectComplexQuery(query);
client/src/annoMatrix/middleware.js → client/src/annoMatrix/middleware.ts
+8 -6
View File
@@ -11,7 +11,7 @@ Undoable metareducer and the AnnoMatrix private API. It would be helpful
to make the Undoable interface better factored.
*/
const annoMatrixGC = (store) => (next) => (action) => {
const annoMatrixGC = (store: any) => (next: any) => (action: any) => {
if (_itIsTimeForGC()) {
_doGC(store);
}
@@ -34,7 +34,7 @@ function _itIsTimeForGC() {
return false;
}
function _doGC(store) {
function _doGC(store: any) {
const state = store.getState();
// these should probably be a function imported from undoable.js, etc, as
@@ -43,8 +43,8 @@ function _doGC(store) {
const undoableFuture = state["@@undoable/future"];
const undoableStack = undoablePast
.concat(undoableFuture)
.flatMap((snapshot) =>
snapshot.filter((v) => v[0] === "annoMatrix").map((v) => v[1])
.flatMap((snapshot: any) =>
snapshot.filter((v: any) => v[0] === "annoMatrix").map((v: any) => v[1])
);
const currentAnnoMatrix = state.annoMatrix;
@@ -53,14 +53,16 @@ function _doGC(store) {
as our current gc algo is more aggressive with those not hot.
*/
const allAnnoMatrices = new Map(
undoableStack.map((m) => [m, { isHot: false }])
undoableStack.map((m: any) => [m, { isHot: false }])
);
let am = currentAnnoMatrix;
while (am) {
allAnnoMatrices.set(am, { isHot: true });
am = am.viewOf;
}
allAnnoMatrices.forEach((hints, annoMatrix) => annoMatrix._gc(hints));
allAnnoMatrices.forEach((hints, annoMatrix) =>
(annoMatrix as any)._gc(hints)
);
}
export default annoMatrixGC;
client/src/annoMatrix/query.js → client/src/annoMatrix/query.ts
+10 -10
View File
@@ -10,7 +10,7 @@ import { _dubEncURIComp } from "./fetchHelpers";
* @param {object | string} query - the query
* @returns {object | string} - the normalized query
*/
export function _queryValidate(query) {
export function _queryValidate(query: any) {
if (typeof query !== "object") return query;
if (query.where && query.summarize)
@@ -40,11 +40,11 @@ export function _queryValidate(query) {
throw new Error("query must specify one of where or summarize");
}
export function _expectSimpleQuery(query) {
export function _expectSimpleQuery(query: any) {
if (typeof query === "object") throw new Error("expected simple query");
}
export function _expectComplexQuery(query) {
export function _expectComplexQuery(query: any) {
if (typeof query !== "object") throw new Error("expected complex query");
}
@@ -55,7 +55,7 @@ export function _expectComplexQuery(query) {
* @param {string|object} query
* @returns the key
*/
export function _queryCacheKey(field, query) {
export function _queryCacheKey(field: any, query: any) {
if (typeof query === "object") {
// complex query
if (query.where) {
@@ -84,22 +84,22 @@ export function _queryCacheKey(field, query) {
return `${field}/${query}`;
}
function _urlEncodeWhereQuery(q) {
function _urlEncodeWhereQuery(q: any) {
const { field: queryField, column: queryColumn, value: queryValue } = q;
return `${_dubEncURIComp(queryField)}:${_dubEncURIComp(
queryColumn
)}=${_dubEncURIComp(queryValue)}`;
}
function _urlEncodeSummarizeQuery(q) {
function _urlEncodeSummarizeQuery(q: any) {
const { method, field, column, values } = q;
const filter = values
.map((value) => _urlEncodeWhereQuery({ field, column, value }))
.map((value: any) => _urlEncodeWhereQuery({ field, column, value }))
.join("&");
return `method=${method}&${filter}`;
}
export function _urlEncodeComplexQuery(q) {
export function _urlEncodeComplexQuery(q: any) {
if (typeof q === "object") {
if (q.where) {
return _urlEncodeWhereQuery(q.where);
@@ -111,7 +111,7 @@ export function _urlEncodeComplexQuery(q) {
throw new Error("Unrecognized complex query type");
}
export function _urlEncodeLabelQuery(colKey, q) {
export function _urlEncodeLabelQuery(colKey: any, q: any) {
if (!colKey) throw new Error("Unsupported query by name");
if (typeof q !== "string") throw new Error("Query must be a simple label.");
return `${colKey}=${encodeURIComponent(q)}`;
@@ -120,7 +120,7 @@ export function _urlEncodeLabelQuery(colKey, q) {
/**
* Generate the column key the server will send us for this query.
*/
export function _hashStringValues(arrayOfString) {
export function _hashStringValues(arrayOfString: any) {
const hash = sha1(arrayOfString.join(""));
return hash;
}
client/src/annoMatrix/schema.js → client/src/annoMatrix/schema.ts
+12 -4
View File
@@ -4,7 +4,7 @@ Private helper functions related to schema
import catLabelSort from "../util/catLabelSort";
import { unassignedCategoryLabel } from "../globals";
export function _getColumnSchema(schema, field, col) {
export function _getColumnSchema(schema: any, field: any, col: any) {
/* look up the column definition */
switch (field) {
case "obs":
@@ -26,7 +26,7 @@ export function _getColumnSchema(schema, field, col) {
}
}
export function _getColumnDimensionNames(schema, field, col) {
export function _getColumnDimensionNames(schema: any, field: any, col: any) {
/*
field/col may be an alias for multiple columns. Currently used to map ND
values to 1D dataframe columns for embeddings/layout. Signified by the presence
@@ -39,6 +39,7 @@ export function _getColumnDimensionNames(schema, field, col) {
return colSchema.dims || [col];
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'schema' implicitly has an 'any' type.
export function _schemaColumns(schema, field) {
switch (field) {
case "obs":
@@ -52,18 +53,25 @@ export function _schemaColumns(schema, field) {
}
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'schema' implicitly has an 'any' type.
export function _getWritableColumns(schema, field) {
if (field !== "obs") return [];
return schema.annotations.obs.columns
return (
schema.annotations.obs.columns
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'v' implicitly has an 'any' type.
.filter((v) => v.writable)
.map((v) => v.name);
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'v' implicitly has an 'any' type.
.map((v) => v.name)
);
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'schema' implicitly has an 'any' type.
export function _isContinuousType(schema) {
const { type } = schema;
return !(type === "string" || type === "boolean" || type === "categorical");
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'colSchema' implicitly has an 'any' type... Remove this comment to see the full error message
export function _normalizeCategoricalSchema(colSchema, col) {
const { type, writable } = colSchema;
if (
client/src/annoMatrix/viewCreators.js → client/src/annoMatrix/viewCreators.ts
+6 -1
View File
@@ -5,7 +5,7 @@ instances of AnnoMatrix, implementing common UI functions.
import { AnnoMatrixRowSubsetView, AnnoMatrixClipView } from "./views";
export function isubsetMask(annoMatrix, obsMask) {
export function isubsetMask(annoMatrix: any, obsMask: any) {
/*
Subset annomatrix to contain the rows which have truish value in the mask.
Maks length must equal annoMatrix.nObs (row count).
@@ -13,6 +13,7 @@ export function isubsetMask(annoMatrix, obsMask) {
return isubset(annoMatrix, _maskToList(obsMask));
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'annoMatrix' implicitly has an 'any' typ... Remove this comment to see the full error message
export function isubset(annoMatrix, obsOffsets) {
/*
Subset annomatrix to contain the positions contained in the obsOffsets array
@@ -25,6 +26,7 @@ export function isubset(annoMatrix, obsOffsets) {
return new AnnoMatrixRowSubsetView(annoMatrix, obsIndex);
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'annoMatrix' implicitly has an 'any' typ... Remove this comment to see the full error message
export function subset(annoMatrix, obsLabels) {
/*
subset based on labels
@@ -33,6 +35,7 @@ export function subset(annoMatrix, obsLabels) {
return new AnnoMatrixRowSubsetView(annoMatrix, obsIndex);
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'annoMatrix' implicitly has an 'any' typ... Remove this comment to see the full error message
export function subsetByIndex(annoMatrix, obsIndex) {
/*
subset based upon the new obs index.
@@ -40,6 +43,7 @@ export function subsetByIndex(annoMatrix, obsIndex) {
return new AnnoMatrixRowSubsetView(annoMatrix, obsIndex);
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'annoMatrix' implicitly has an 'any' typ... Remove this comment to see the full error message
export function clip(annoMatrix, qmin, qmax) {
/*
Create a view that clips all continuous data to the [min, max] range.
@@ -53,6 +57,7 @@ export function clip(annoMatrix, qmin, qmax) {
Private utility functions below
*/
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'mask' implicitly has an 'any' type.
function _maskToList(mask) {
/* convert masks to lists - method wastes space, but is fast */
if (!mask) {
client/src/annoMatrix/views.js → client/src/annoMatrix/views.ts
+26 -13
View File
@@ -9,21 +9,26 @@ import { _whereCacheCreate } from "./whereCache";
import { _isContinuousType, _getColumnSchema } from "./schema";
class AnnoMatrixView extends AnnoMatrix {
constructor(viewOf, rowIndex = null) {
constructor(viewOf: any, rowIndex = null) {
// @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
const nObs = rowIndex ? rowIndex.size() : viewOf.nObs;
super(viewOf.schema, nObs, viewOf.nVar, rowIndex || viewOf.rowIndex);
this.viewOf = viewOf;
this.isView = true;
}
addObsAnnoCategory(col, category) {
addObsAnnoCategory(col: any, category: any) {
const newAnnoMatrix = this._clone();
newAnnoMatrix.viewOf = this.viewOf.addObsAnnoCategory(col, category);
newAnnoMatrix.schema = newAnnoMatrix.viewOf.schema;
return newAnnoMatrix;
}
async removeObsAnnoCategory(col, category, unassignedCategory) {
async removeObsAnnoCategory(
col: any,
category: any,
unassignedCategory: any
) {
const newAnnoMatrix = this._clone();
newAnnoMatrix.viewOf = await this.viewOf.removeObsAnnoCategory(
col,
@@ -34,7 +39,7 @@ class AnnoMatrixView extends AnnoMatrix {
return newAnnoMatrix;
}
dropObsColumn(col) {
dropObsColumn(col: any) {
const newAnnoMatrix = this._clone();
newAnnoMatrix.viewOf = this.viewOf.dropObsColumn(col);
newAnnoMatrix._cache.obs = this._cache.obs.dropCol(col);
@@ -42,21 +47,21 @@ class AnnoMatrixView extends AnnoMatrix {
return newAnnoMatrix;
}
addObsColumn(colSchema, Ctor, value) {
addObsColumn(colSchema: any, Ctor: any, value: any) {
const newAnnoMatrix = this._clone();
newAnnoMatrix.viewOf = this.viewOf.addObsColumn(colSchema, Ctor, value);
newAnnoMatrix.schema = newAnnoMatrix.viewOf.schema;
return newAnnoMatrix;
}
renameObsColumn(oldCol, newCol) {
renameObsColumn(oldCol: any, newCol: any) {
const newAnnoMatrix = this._clone();
newAnnoMatrix.viewOf = this.viewOf.renameObsColumn(oldCol, newCol);
newAnnoMatrix.schema = newAnnoMatrix.viewOf.schema;
return newAnnoMatrix;
}
async setObsColumnValues(col, rowLabels, value) {
async setObsColumnValues(col: any, rowLabels: any, value: any) {
const newAnnoMatrix = this._clone();
newAnnoMatrix.viewOf = await this.viewOf.setObsColumnValues(
col,
@@ -68,7 +73,7 @@ class AnnoMatrixView extends AnnoMatrix {
return newAnnoMatrix;
}
async resetObsColumnValues(col, oldValue, newValue) {
async resetObsColumnValues(col: any, oldValue: any, newValue: any) {
const newAnnoMatrix = this._clone();
newAnnoMatrix.viewOf = await this.viewOf.resetObsColumnValues(
col,
@@ -80,7 +85,7 @@ class AnnoMatrixView extends AnnoMatrix {
return newAnnoMatrix;
}
addEmbedding(colSchema) {
addEmbedding(colSchema: any) {
const newAnnoMatrix = this._clone();
newAnnoMatrix.viewOf = this.viewOf.addEmbedding(colSchema);
newAnnoMatrix.schema = newAnnoMatrix.viewOf.schema;
@@ -92,17 +97,20 @@ class AnnoMatrixMapView extends AnnoMatrixView {
/*
A view which knows how to transform its data.
*/
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'viewOf' implicitly has an 'any' type.
constructor(viewOf, mapFn) {
super(viewOf);
this.mapFn = mapFn;
(this as any).mapFn = mapFn;
}
// @ts-expect-error ts-migrate(2416) FIXME: Property '_doLoad' in type 'AnnoMatrixMapView' is ... Remove this comment to see the full error message
async _doLoad(field, query) {
const df = await this.viewOf._fetch(field, query);
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'colData' implicitly has an 'any' type.
const dfMapped = df.mapColumns((colData, colIdx) => {
const colLabel = df.colIndex.getLabel(colIdx);
const colSchema = _getColumnSchema(this.schema, field, colLabel);
return this.mapFn(field, colLabel, colSchema, colData, df);
return (this as any).mapFn(field, colLabel, colSchema, colData, df);
});
const whereCacheUpdate = _whereCacheCreate(
field,
@@ -117,12 +125,14 @@ export class AnnoMatrixClipView extends AnnoMatrixMapView {
/*
A view which is a clipped transformation of its parent
*/
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'viewOf' implicitly has an 'any' type.
constructor(viewOf, qmin, qmax) {
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
super(viewOf, (field, colLabel, colSchema, colData, df) =>
_clipAnnoMatrix(field, colLabel, colSchema, colData, df, qmin, qmax)
);
this.isClipped = true;
this.clipRange = [qmin, qmax];
(this as any).isClipped = true;
(this as any).clipRange = [qmin, qmax];
Object.seal(this);
}
}
@@ -131,11 +141,13 @@ export class AnnoMatrixRowSubsetView extends AnnoMatrixView {
/*
A view which is a subset of total rows.
*/
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'viewOf' implicitly has an 'any' type.
constructor(viewOf, rowIndex) {
super(viewOf, rowIndex);
Object.seal(this);
}
// @ts-expect-error ts-migrate(2416) FIXME: Property '_doLoad' in type 'AnnoMatrixRowSubsetVie... Remove this comment to see the full error message
async _doLoad(field, query) {
const df = await this.viewOf._fetch(field, query);
@@ -158,6 +170,7 @@ export class AnnoMatrixRowSubsetView extends AnnoMatrixView {
Utility functions below
*/
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
function _clipAnnoMatrix(field, colLabel, colSchema, colData, df, qmin, qmax) {
/* only clip obs and var scalar columns */
if (field !== "obs" && field !== "X") return colData;
client/src/annoMatrix/whereCache.js → client/src/annoMatrix/whereCache.ts
+12 -2
View File
@@ -51,7 +51,12 @@ creates a cache entry of:
import { _getColumnDimensionNames } from "./schema";
import { _hashStringValues } from "./query";
export function _whereCacheGet(whereCache, schema, field, query) {
export function _whereCacheGet(
whereCache: any,
schema: any,
field: any,
query: any
) {
/*
query will either be an where query (object) or a column name (string).
@@ -85,6 +90,7 @@ export function _whereCacheGet(whereCache, schema, field, query) {
return _getColumnDimensionNames(schema, field, query) ?? [undefined];
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type.
export function _whereCacheCreate(field, query, columnLabels) {
/*
Create a new whereCache
@@ -131,10 +137,11 @@ export function _whereCacheCreate(field, query, columnLabels) {
return {};
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'dst' implicitly has an 'any' type.
function __mergeQueries(dst, src) {
for (const [queryField, columnMap] of Object.entries(src)) {
dst[queryField] = dst[queryField] || new Map();
for (const [queryColumn, valueMap] of columnMap) {
for (const [queryColumn, valueMap] of columnMap as any) {
if (!dst[queryField].has(queryColumn))
dst[queryField].set(queryColumn, new Map());
for (const [queryValue, columnLabels] of valueMap) {
@@ -144,6 +151,7 @@ function __mergeQueries(dst, src) {
}
}
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'dst' implicitly has an 'any' type.
function __whereCacheMerge(dst, src) {
/*
merge src into dst (modifies dst)
@@ -161,6 +169,7 @@ function __whereCacheMerge(dst, src) {
dst.summarize = dst.summarize || {};
for (const [field, method] of Object.entries(src.summarize)) {
dst.summarize[field] = dst.summarize[field] || {};
// @ts-expect-error ts-migrate(2769) FIXME: No overload matches this call.
for (const [methodName, query] of Object.entries(method)) {
dst.summarize[field][methodName] =
dst.summarize[field][methodName] || {};
@@ -171,6 +180,7 @@ function __whereCacheMerge(dst, src) {
return dst;
}
// @ts-expect-error ts-migrate(7019) FIXME: Rest parameter 'caches' implicitly has an 'any[]' ... Remove this comment to see the full error message
export function _whereCacheMerge(...caches) {
return caches.reduce(__whereCacheMerge, {});
}
client/src/components/annoDialog.js → client/src/components/annoDialog.tsx
+21 -2
View File
@@ -1,30 +1,49 @@
import React from "react";
import { Button, Tooltip, Dialog, Classes, Colors } from "@blueprintjs/core";
class AnnoDialog extends React.PureComponent {
constructor(props) {
type State = any;
class AnnoDialog extends React.PureComponent<{}, State> {
constructor(props: {}) {
super(props);
this.state = {};
}
render() {
const {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isActive' does not exist on type 'Readon... Remove this comment to see the full error message
isActive,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'text' does not exist on type 'Readonly<{... Remove this comment to see the full error message
text,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'title' does not exist on type 'Readonly<... Remove this comment to see the full error message
title,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'instruction' does not exist on type 'Rea... Remove this comment to see the full error message
instruction,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'cancelTooltipContent' does not exist on ... Remove this comment to see the full error message
cancelTooltipContent,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'errorMessage' does not exist on type 'Re... Remove this comment to see the full error message
errorMessage,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'validationError' does not exist on type ... Remove this comment to see the full error message
validationError,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'annoSelect' does not exist on type 'Read... Remove this comment to see the full error message
annoSelect,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'annoInput' does not exist on type 'Reado... Remove this comment to see the full error message
annoInput,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'secondaryInstructions' does not exist on... Remove this comment to see the full error message
secondaryInstructions,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'secondaryInput' does not exist on type '... Remove this comment to see the full error message
secondaryInput,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'handleCancel' does not exist on type 'Re... Remove this comment to see the full error message
handleCancel,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'handleSubmit' does not exist on type 'Re... Remove this comment to see the full error message
handleSubmit,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'primaryButtonText' does not exist on typ... Remove this comment to see the full error message
primaryButtonText,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'secondaryButtonText' does not exist on t... Remove this comment to see the full error message
secondaryButtonText,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'handleSecondaryButtonSubmit' does not ex... Remove this comment to see the full error message
handleSecondaryButtonSubmit,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'primaryButtonProps' does not exist on ty... Remove this comment to see the full error message
primaryButtonProps,
} = this.props;
client/src/components/app.js → client/src/components/app.tsx
+11 -7
View File
@@ -15,30 +15,32 @@ import TermsOfServicePrompt from "./termsPrompt";
import actions from "../actions";
// @ts-expect-error ts-migrate(1238) FIXME: Unable to resolve signature of class decorator whe... Remove this comment to see the full error message
@connect((state) => ({
loading: state.controls.loading,
error: state.controls.error,
graphRenderCounter: state.controls.graphRenderCounter,
loading: (state as any).controls.loading,
error: (state as any).controls.error,
graphRenderCounter: (state as any).controls.graphRenderCounter,
}))
class App extends React.Component {
componentDidMount() {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message
const { dispatch } = this.props;
/* listen for url changes, fire one when we start the app up */
window.addEventListener("popstate", this._onURLChanged);
this._onURLChanged();
// @ts-expect-error ts-migrate(2554) FIXME: Expected 0 arguments, but got 1.
dispatch(actions.doInitialDataLoad(window.location.search));
this.forceUpdate();
}
_onURLChanged() {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message
const { dispatch } = this.props;
dispatch({ type: "url changed", url: document.location.href });
}
render() {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'loading' does not exist on type 'Readonl... Remove this comment to see the full error message
const { loading, error, graphRenderCounter } = this.props;
return (
<Container>
@@ -70,13 +72,15 @@ class App extends React.Component {
{loading || error ? null : (
<Layout>
<LeftSideBar />
{(viewportRef) => (
{(viewportRef: any) => (
<>
<MenuBar />
<Embedding />
<Autosave />
<TermsOfServicePrompt />
{/* @ts-expect-error ts-migrate(2769) FIXME: No overload matches this call. */}
<Legend viewportRef={viewportRef} />
{/* @ts-expect-error ts-migrate(2322) FIXME: Type '{ key: any; viewportRef: any; }' is not assi... Remove this comment to see the full error message */}
<Graph key={graphRenderCounter} viewportRef={viewportRef} />
</>
)}
client/src/components/autosave/filenameDialog.js → client/src/components/autosave/filenameDialog.tsx
+27 -13
View File
@@ -11,18 +11,23 @@ import {
Tooltip,
} from "@blueprintjs/core";
type State = any;
// @ts-expect-error ts-migrate(1238) FIXME: Unable to resolve signature of class decorator whe... Remove this comment to see the full error message
@connect((state) => ({
idhash: state.config?.parameters?.["annotations-user-data-idhash"] ?? null,
annotations: state.annotations,
auth: state.config?.authentication,
userInfo: state.userInfo,
writableCategoriesEnabled: state.config?.parameters?.annotations ?? false,
idhash:
(state as any).config?.parameters?.["annotations-user-data-idhash"] ?? null,
annotations: (state as any).annotations,
auth: (state as any).config?.authentication,
userInfo: (state as any).userInfo,
writableCategoriesEnabled:
(state as any).config?.parameters?.annotations ?? false,
writableGenesetsEnabled: !(
state.config?.parameters?.annotations_genesets_readonly ?? true
(state as any).config?.parameters?.annotations_genesets_readonly ?? true
),
}))
class FilenameDialog extends React.Component {
constructor(props) {
class FilenameDialog extends React.Component<{}, State> {
constructor(props: {}) {
super(props);
this.state = {
filenameText: "",
@@ -32,9 +37,9 @@ class FilenameDialog extends React.Component {
dismissFilenameDialog = () => {};
handleCreateFilename = () => {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message
const { dispatch } = this.props;
const { filenameText } = this.state;
dispatch({
type: "set annotations collection name",
data: filenameText,
@@ -45,8 +50,8 @@ class FilenameDialog extends React.Component {
const legalNames = /^\w+$/;
const { filenameText } = this.state;
let err = false;
if (filenameText === "") {
// @ts-expect-error ts-migrate(2322) FIXME: Type 'string' is not assignable to type 'boolean'.
err = "empty_string";
} else if (!legalNames.test(filenameText)) {
/*
@@ -55,16 +60,16 @@ class FilenameDialog extends React.Component {
from the data collection name. If you change this, you will also need
to change the validation code in the backend, or it will have no effect.
*/
// @ts-expect-error ts-migrate(2322) FIXME: Type 'string' is not assignable to type 'boolean'.
err = "characters";
}
return err;
};
filenameErrorMessage = () => {
const err = this.filenameError();
let markup = null;
// @ts-expect-error ts-migrate(2367) FIXME: This condition will always return 'false' since th... Remove this comment to see the full error message
if (err === "empty_string") {
markup = (
<span
@@ -78,6 +83,7 @@ class FilenameDialog extends React.Component {
Name cannot be blank
</span>
);
// @ts-expect-error ts-migrate(2367) FIXME: This condition will always return 'false' since th... Remove this comment to see the full error message
} else if (err === "characters") {
markup = (
<span
@@ -97,14 +103,18 @@ class FilenameDialog extends React.Component {
render() {
const {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'writableCategoriesEnabled' does not exis... Remove this comment to see the full error message
writableCategoriesEnabled,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'writableGenesetsEnabled' does not exist ... Remove this comment to see the full error message
writableGenesetsEnabled,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'annotations' does not exist on type 'Rea... Remove this comment to see the full error message
annotations,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'idhash' does not exist on type 'Readonly... Remove this comment to see the full error message
idhash,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'userInfo' does not exist on type 'Readon... Remove this comment to see the full error message
userInfo,
} = this.props;
const { filenameText } = this.state;
return (writableCategoriesEnabled || writableGenesetsEnabled) &&
annotations.promptForFilename &&
!annotations.dataCollectionNameIsReadOnly &&
@@ -128,6 +138,7 @@ class FilenameDialog extends React.Component {
<InputGroup
autoFocus
value={filenameText}
// @ts-expect-error ts-migrate(2554) FIXME: Expected 0 arguments, but got 1.
intent={this.filenameError(filenameText) ? "warning" : "none"}
onChange={(e) =>
this.setState({ filenameText: e.target.value })
@@ -138,12 +149,14 @@ class FilenameDialog extends React.Component {
<p
style={{
marginTop: 7,
// @ts-expect-error ts-migrate(2554) FIXME: Expected 0 arguments, but got 1.
visibility: this.filenameError(filenameText)
? "visible"
: "hidden",
color: Colors.ORANGE3,
}}
>
{/* @ts-expect-error ts-migrate(2554) FIXME: Expected 0 arguments, but got 1. */}
{this.filenameErrorMessage(filenameText)}
</p>
</div>
@@ -171,6 +184,7 @@ class FilenameDialog extends React.Component {
<Button onClick={this.dismissFilenameDialog}>Cancel</Button>
</Tooltip>
<Button
// @ts-expect-error ts-migrate(2554) FIXME: Expected 0 arguments, but got 1.
disabled={!filenameText || this.filenameError(filenameText)}
onClick={this.handleCreateFilename}
intent="primary"
client/src/components/autosave/index.js → client/src/components/autosave/index.tsx
+30 -15
View File
@@ -3,23 +3,30 @@ import { connect } from "react-redux";
import actions from "../../actions";
import FilenameDialog from "./filenameDialog";
type State = any;
// @ts-expect-error ts-migrate(1238) FIXME: Unable to resolve signature of class decorator whe... Remove this comment to see the full error message
@connect((state) => ({
annotations: state.annotations,
annotations: (state as any).annotations,
obsAnnotationSaveInProgress:
state.autosave?.obsAnnotationSaveInProgress ?? false,
genesetSaveInProgress: state.autosave?.genesetSaveInProgress ?? false,
error: state.autosave?.error,
writableCategoriesEnabled: state.config?.parameters?.annotations ?? false,
(state as any).autosave?.obsAnnotationSaveInProgress ?? false,
genesetSaveInProgress:
(state as any).autosave?.genesetSaveInProgress ?? false,
error: (state as any).autosave?.error,
writableCategoriesEnabled:
(state as any).config?.parameters?.annotations ?? false,
writableGenesetsEnabled: !(
state.config?.parameters?.annotations_genesets_readonly ?? true
(state as any).config?.parameters?.annotations_genesets_readonly ?? true
),
annoMatrix: state.annoMatrix,
genesets: state.genesets,
lastSavedAnnoMatrix: state.autosave?.lastSavedAnnoMatrix,
lastSavedGenesets: state.autosave?.lastSavedGenesets,
annoMatrix: (state as any).annoMatrix,
genesets: (state as any).genesets,
lastSavedAnnoMatrix: (state as any).autosave?.lastSavedAnnoMatrix,
lastSavedGenesets: (state as any).autosave?.lastSavedGenesets,
}))
class Autosave extends React.Component {
constructor(props) {
class Autosave extends React.Component<{}, State> {
clearInterval: any;
constructor(props: {}) {
super(props);
this.state = {
timer: null,
@@ -27,8 +34,8 @@ class Autosave extends React.Component {
}
componentDidMount() {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'writableCategoriesEnabled' does not exis... Remove this comment to see the full error message
const { writableCategoriesEnabled, writableGenesetsEnabled } = this.props;
let { timer } = this.state;
if (timer) clearInterval(timer);
if (writableCategoriesEnabled || writableGenesetsEnabled) {
@@ -46,8 +53,11 @@ class Autosave extends React.Component {
tick = () => {
const {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message
dispatch,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'obsAnnotationSaveInProgress' does not ex... Remove this comment to see the full error message
obsAnnotationSaveInProgress,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'genesetSaveInProgress' does not exist on... Remove this comment to see the full error message
genesetSaveInProgress,
} = this.props;
if (!obsAnnotationSaveInProgress && this.needToSaveObsAnnotations()) {
@@ -60,12 +70,14 @@ class Autosave extends React.Component {
needToSaveObsAnnotations = () => {
/* return true if we need to save obs cell labels, false if we don't */
// @ts-expect-error ts-migrate(2339) FIXME: Property 'annoMatrix' does not exist on type 'Read... Remove this comment to see the full error message
const { annoMatrix, lastSavedAnnoMatrix } = this.props;
return actions.needToSaveObsAnnotations(annoMatrix, lastSavedAnnoMatrix);
};
needToSaveGenesets = () => {
/* return true if we need to save gene ses, false if we do not */
// @ts-expect-error ts-migrate(2339) FIXME: Property 'genesets' does not exist on type 'Readon... Remove this comment to see the full error message
const { genesets, lastSavedGenesets } = this.props;
return genesets.initialized && genesets.genesets !== lastSavedGenesets;
};
@@ -75,11 +87,13 @@ class Autosave extends React.Component {
}
saveInProgress() {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'obsAnnotationSaveInProgress' does not ex... Remove this comment to see the full error message
const { obsAnnotationSaveInProgress, genesetSaveInProgress } = this.props;
return obsAnnotationSaveInProgress || genesetSaveInProgress;
}
statusMessage() {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'error' does not exist on type 'Readonly<... Remove this comment to see the full error message
const { error } = this.props;
if (error) {
return `Autosave error: ${error}`;
@@ -89,14 +103,15 @@ class Autosave extends React.Component {
render() {
const {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'writableCategoriesEnabled' does not exis... Remove this comment to see the full error message
writableCategoriesEnabled,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'writableGenesetsEnabled' does not exist ... Remove this comment to see the full error message
writableGenesetsEnabled,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'lastSavedAnnoMatrix' does not exist on t... Remove this comment to see the full error message
lastSavedAnnoMatrix,
} = this.props;
const initialDataLoadComplete = lastSavedAnnoMatrix;
if (!writableCategoriesEnabled && !writableGenesetsEnabled) return null;
return (
<div
id="autosave"
client/src/components/brushableHistogram/error.js → client/src/components/brushableHistogram/error.tsx
+1 -1
View File
@@ -1,7 +1,7 @@
import React from "react";
import * as globals from "../../globals";
const ErrorLoading = ({ displayName, zebra }) => {
const ErrorLoading = ({ displayName, zebra }: any) => {
return (
<div
style={{
client/src/components/brushableHistogram/footer.js → client/src/components/brushableHistogram/footer.tsx
+8
View File
@@ -2,13 +2,21 @@ import React from "react";
const HistogramFooter = React.memo(
({
// @ts-expect-error ts-migrate(2339) FIXME: Property 'displayName' does not exist on type '{ c... Remove this comment to see the full error message
displayName,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'hideRanges' does not exist on type '{ ch... Remove this comment to see the full error message
hideRanges,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'rangeMin' does not exist on type '{ chil... Remove this comment to see the full error message
rangeMin,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'rangeMax' does not exist on type '{ chil... Remove this comment to see the full error message
rangeMax,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'rangeColorMin' does not exist on type '{... Remove this comment to see the full error message
rangeColorMin,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'rangeColorMax' does not exist on type '{... Remove this comment to see the full error message
rangeColorMax,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isObs' does not exist on type '{ childre... Remove this comment to see the full error message
isObs,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isGeneSetSummary' does not exist on type... Remove this comment to see the full error message
isGeneSetSummary,
}) => {
/*
client/src/components/brushableHistogram/header.js → client/src/components/brushableHistogram/header.tsx
+9
View File
@@ -5,14 +5,23 @@ import * as globals from "../../globals";
const HistogramHeader = React.memo(
({
// @ts-expect-error ts-migrate(2339) FIXME: Property 'fieldId' does not exist on type '{ child... Remove this comment to see the full error message
fieldId,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isColorBy' does not exist on type '{ chi... Remove this comment to see the full error message
isColorBy,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'onColorByClick' does not exist on type '... Remove this comment to see the full error message
onColorByClick,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'onRemoveClick' does not exist on type '{... Remove this comment to see the full error message
onRemoveClick,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isScatterPlotX' does not exist on type '... Remove this comment to see the full error message
isScatterPlotX,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isScatterPlotY' does not exist on type '... Remove this comment to see the full error message
isScatterPlotY,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'onScatterPlotXClick' does not exist on t... Remove this comment to see the full error message
onScatterPlotXClick,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'onScatterPlotYClick' does not exist on t... Remove this comment to see the full error message
onScatterPlotYClick,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isObs' does not exist on type '{ childre... Remove this comment to see the full error message
isObs,
}) => {
/*
client/src/components/brushableHistogram/histogram.js → client/src/components/brushableHistogram/histogram.tsx
+14 -3
View File
@@ -18,7 +18,7 @@ const Histogram = ({
isColorBy,
selectionRange,
mini,
}) => {
}: any) => {
const svgRef = useRef(null);
const [brush, setBrush] = useState(null);
@@ -69,14 +69,18 @@ const Histogram = ({
.data(bins)
.enter()
.append("rect")
// @ts-expect-error ts-migrate(6133) FIXME: 'd' is declared but its value is never read.
.attr("x", (d, i) => x(binStart(i)) + 1)
.attr("y", (d) => y(d))
// @ts-expect-error ts-migrate(6133) FIXME: 'd' is declared but its value is never read.
.attr("width", (d, i) => x(binEnd(i)) - x(binStart(i)) - binPadding)
.attr("height", (d) => y(0) - y(d))
.style(
"fill",
// @ts-expect-error ts-migrate(2769) FIXME: No overload matches this call.
isColorBy
? (d, i) => colorScale(histogramScale(binStart(i)))
? // @ts-expect-error ts-migrate(6133) FIXME: 'd' is declared but its value is never read.
(d: any, i: any) => colorScale(histogramScale(binStart(i)))
: defaultBarColor
);
}
@@ -101,6 +105,7 @@ const Histogram = ({
const brushXselection = container
.insert("g")
.attr("class", "brush")
// @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
.attr("data-testid", `${svgRef.current.dataset.testid}-brushable-area`)
.call(brushX);
@@ -113,6 +118,7 @@ const Histogram = ({
d3
.axisBottom(x)
.ticks(4)
// @ts-expect-error ts-migrate(2769) FIXME: No overload matches this call.
.tickFormat(d3.format(maybeScientific(x)))
);
@@ -126,8 +132,9 @@ const Histogram = ({
.axisRight(y)
.ticks(3)
.tickFormat(
// @ts-expect-error ts-migrate(2769) FIXME: No overload matches this call.
d3.format(
y.domain().some((n) => Math.abs(n) >= 10000) ? ".0e" : ","
y.domain().some((n: any) => Math.abs(n) >= 10000) ? ".0e" : ","
)
)
);
@@ -137,6 +144,7 @@ const Histogram = ({
svg.selectAll(".axis path").style("stroke", "rgb(230,230,230)");
svg.selectAll(".axis line").style("stroke", "rgb(230,230,230)");
// @ts-expect-error ts-migrate(2345) FIXME: Argument of type '{ brushX: d3.BrushBehavior<unkno... Remove this comment to see the full error message
setBrush({ brushX, brushXselection });
}
}, [histogram, isColorBy]);
@@ -146,6 +154,7 @@ const Histogram = ({
paint/update selection brush
*/
if (!brush) return;
// @ts-expect-error ts-migrate(2339) FIXME: Property 'brushX' does not exist on type 'null'.
const { brushX, brushXselection } = brush;
const selection = d3.brushSelection(brushXselection.node());
if (!selectionRange && selection) {
@@ -162,7 +171,9 @@ const Histogram = ({
} else {
/* there is an active selection and a brush - make sure they match */
const moveDeltaThreshold = 1;
// @ts-expect-error ts-migrate(2363) FIXME: The right-hand side of an arithmetic operation mus... Remove this comment to see the full error message
const dX0 = Math.abs(x0 - selection[0]);
// @ts-expect-error ts-migrate(2363) FIXME: The right-hand side of an arithmetic operation mus... Remove this comment to see the full error message
const dX1 = Math.abs(x1 - selection[1]);
/*
only update the brush if it is grossly incorrect,
client/src/components/brushableHistogram/index.js → client/src/components/brushableHistogram/index.tsx
+95 -58
View File
@@ -29,27 +29,31 @@ const MARGIN_MINI = {
const WIDTH_MINI = 120 - MARGIN_MINI.LEFT - MARGIN_MINI.RIGHT;
const HEIGHT_MINI = 15 - MARGIN_MINI.TOP - MARGIN_MINI.BOTTOM;
// @ts-expect-error ts-migrate(1238) FIXME: Unable to resolve signature of class decorator whe... Remove this comment to see the full error message
@connect((state, ownProps) => {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isObs' does not exist on type '{}'.
const { isObs, isUserDefined, isGeneSetSummary, field } = ownProps;
const myName = makeContinuousDimensionName(
{ isObs, isUserDefined, isGeneSetSummary },
field
);
return {
annoMatrix: state.annoMatrix,
isScatterplotXXaccessor: state.controls.scatterplotXXaccessor === field,
isScatterplotYYaccessor: state.controls.scatterplotYYaccessor === field,
continuousSelectionRange: state.continuousSelection[myName],
isColorAccessor: state.colors.colorAccessor === field,
annoMatrix: (state as any).annoMatrix,
isScatterplotXXaccessor:
(state as any).controls.scatterplotXXaccessor === field,
isScatterplotYYaccessor:
(state as any).controls.scatterplotYYaccessor === field,
continuousSelectionRange: (state as any).continuousSelection[myName],
isColorAccessor: (state as any).colors.colorAccessor === field,
};
})
class HistogramBrush extends React.PureComponent {
static watchAsync(props, prevProps) {
static watchAsync(props: any, prevProps: any) {
return !shallowEqual(props.watchProps, prevProps.watchProps);
}
/* memoized closure to prevent HistogramHeader unecessary repaint */
handleColorAction = memoize((dispatch) => (field, isObs) => {
handleColorAction = memoize((dispatch) => (field: any, isObs: any) => {
if (isObs) {
dispatch({
type: "color by continuous metadata",
@@ -60,25 +64,31 @@ class HistogramBrush extends React.PureComponent {
}
});
onBrush = (selection, x, eventType) => {
// @ts-expect-error ts-migrate(6133) FIXME: 'selection' is declared but its value is never rea... Remove this comment to see the full error message
onBrush = (selection: any, x: any, eventType: any) => {
const type = `continuous metadata histogram ${eventType}`;
return () => {
const {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message
dispatch,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'field' does not exist on type 'Readonly<... Remove this comment to see the full error message
field,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isObs' does not exist on type 'Readonly<... Remove this comment to see the full error message
isObs,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isUserDefined' does not exist on type 'R... Remove this comment to see the full error message
isUserDefined,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isGeneSetSummary' does not exist on type... Remove this comment to see the full error message
isGeneSetSummary,
} = this.props;
// ignore programmatically generated events
if (!d3.event.sourceEvent) return;
if (!(d3 as any).event.sourceEvent) return;
// ignore cascading events, which are programmatically generated
if (d3.event.sourceEvent.sourceEvent) return;
if ((d3 as any).event.sourceEvent.sourceEvent) return;
const query = this.createQuery();
const range = d3.event.selection
? [x(d3.event.selection[0]), x(d3.event.selection[1])]
const range = (d3 as any).event.selection
? [x((d3 as any).event.selection[0]), x((d3 as any).event.selection[1])]
: null;
const otherProps = {
selection: field,
@@ -94,42 +104,52 @@ class HistogramBrush extends React.PureComponent {
};
};
onBrushEnd = (selection, x) => {
// @ts-expect-error ts-migrate(6133) FIXME: 'selection' is declared but its value is never rea... Remove this comment to see the full error message
onBrushEnd = (selection: any, x: any) => {
return () => {
const {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message
dispatch,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'field' does not exist on type 'Readonly<... Remove this comment to see the full error message
field,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isObs' does not exist on type 'Readonly<... Remove this comment to see the full error message
isObs,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isUserDefined' does not exist on type 'R... Remove this comment to see the full error message
isUserDefined,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isGeneSetSummary' does not exist on type... Remove this comment to see the full error message
isGeneSetSummary,
} = this.props;
const minAllowedBrushSize = 10;
const smallAmountToAvoidInfiniteLoop = 0.1;
// ignore programmatically generated events
if (!d3.event.sourceEvent) return;
if (!(d3 as any).event.sourceEvent) return;
// ignore cascading events, which are programmatically generated
if (d3.event.sourceEvent.sourceEvent) return;
if ((d3 as any).event.sourceEvent.sourceEvent) return;
let type;
let range = null;
if (d3.event.selection) {
if ((d3 as any).event.selection) {
type = "continuous metadata histogram end";
if (
d3.event.selection[1] - d3.event.selection[0] >
(d3 as any).event.selection[1] - (d3 as any).event.selection[0] >
minAllowedBrushSize
) {
range = [x(d3.event.selection[0]), x(d3.event.selection[1])];
range = [
x((d3 as any).event.selection[0]),
x((d3 as any).event.selection[1]),
];
} else {
/* the user selected range is too small and will be hidden #587, so take control of it procedurally */
/* https://stackoverflow.com/questions/12354729/d3-js-limit-size-of-brush */
const procedurallyResizedBrushWidth =
d3.event.selection[0] +
(d3 as any).event.selection[0] +
minAllowedBrushSize +
smallAmountToAvoidInfiniteLoop; //
range = [x(d3.event.selection[0]), x(procedurallyResizedBrushWidth)];
range = [
x((d3 as any).event.selection[0]),
x(procedurallyResizedBrushWidth),
];
}
} else {
type = "continuous metadata histogram cancel";
@@ -151,6 +171,7 @@ class HistogramBrush extends React.PureComponent {
};
handleSetGeneAsScatterplotX = () => {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message
const { dispatch, field } = this.props;
dispatch({
type: "set scatterplot x",
@@ -159,6 +180,7 @@ class HistogramBrush extends React.PureComponent {
};
handleSetGeneAsScatterplotY = () => {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message
const { dispatch, field } = this.props;
dispatch({
type: "set scatterplot y",
@@ -168,10 +190,15 @@ class HistogramBrush extends React.PureComponent {
removeHistogram = () => {
const {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message
dispatch,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'field' does not exist on type 'Readonly<... Remove this comment to see the full error message
field,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isColorAccessor' does not exist on type ... Remove this comment to see the full error message
isColorAccessor,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isScatterplotXXaccessor' does not exist ... Remove this comment to see the full error message
isScatterplotXXaccessor,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isScatterplotYYaccessor' does not exist ... Remove this comment to see the full error message
isScatterplotYYaccessor,
} = this.props;
dispatch({
@@ -198,11 +225,13 @@ class HistogramBrush extends React.PureComponent {
};
fetchAsyncProps = async () => {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'annoMatrix' does not exist on type 'Read... Remove this comment to see the full error message
const { annoMatrix, width } = this.props;
const { isClipped } = annoMatrix;
const query = this.createQuery();
// @ts-expect-error ts-migrate(2488) FIXME: Type 'any[] | null' must have a '[Symbol.iterator]... Remove this comment to see the full error message
const df = await annoMatrix.fetch(...query);
const column = df.icol(0);
@@ -261,7 +290,7 @@ class HistogramBrush extends React.PureComponent {
};
// eslint-disable-next-line class-methods-use-this -- instance method allows for memoization per annotation
calcHistogramCache(col, newMargin, newWidth, newHeight) {
calcHistogramCache(col: any, newMargin: any, newWidth: any, newHeight: any) {
/*
recalculate expensive stuff, notably bins, summaries, etc.
*/
@@ -269,35 +298,30 @@ class HistogramBrush extends React.PureComponent {
const summary = col.summarize(); /* this is memoized, so it's free the second time you call it */
const { min: domainMin, max: domainMax } = summary;
const numBins = 40;
const {
TOP: topMargin,
LEFT: leftMargin,
} = newMargin; /* changes with mini */
histogramCache.domain = [
domainMin,
domainMax,
]; /* doesn't change with mini */
histogramCache.x = d3
const { TOP: topMargin, LEFT: leftMargin } = newMargin;
(histogramCache as any).domain = [domainMin, domainMax];
/* doesn't change with mini */ (histogramCache as any).x = d3
.scaleLinear()
.domain([domainMin, domainMax])
.range([leftMargin, leftMargin + newWidth]);
histogramCache.bins = col.histogram(numBins, [
(histogramCache as any).bins = col.histogram(numBins, [
domainMin,
domainMax,
]); /* memoized */
]);
/* memoized */ (histogramCache as any).binWidth =
(domainMax - domainMin) / numBins;
histogramCache.binWidth = (domainMax - domainMin) / numBins;
(histogramCache as any).binStart = (i: any) =>
domainMin + i * (histogramCache as any).binWidth;
(histogramCache as any).binEnd = (i: any) =>
domainMin + (i + 1) * (histogramCache as any).binWidth;
histogramCache.binStart = (i) => domainMin + i * histogramCache.binWidth;
histogramCache.binEnd = (i) =>
domainMin + (i + 1) * histogramCache.binWidth;
const yMax = (histogramCache as any).bins.reduce((l: any, r: any) =>
l > r ? l : r
);
const yMax = histogramCache.bins.reduce((l, r) => (l > r ? l : r));
histogramCache.y = d3
(histogramCache as any).y = d3
.scaleLinear()
.domain([0, yMax])
.range([topMargin + newHeight, topMargin]);
@@ -306,13 +330,8 @@ class HistogramBrush extends React.PureComponent {
}
createQuery() {
const {
isObs,
isGeneSetSummary,
field,
setGenes,
annoMatrix,
} = this.props;
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isObs' does not exist on type 'Readonly<... Remove this comment to see the full error message
const { isObs, isGeneSetSummary, field, setGenes, annoMatrix } = this.props;
const { schema } = annoMatrix;
if (isObs) {
return ["obs", field];
@@ -349,21 +368,35 @@ class HistogramBrush extends React.PureComponent {
render() {
const {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message
dispatch,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'annoMatrix' does not exist on type 'Read... Remove this comment to see the full error message
annoMatrix,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'field' does not exist on type 'Readonly<... Remove this comment to see the full error message
field,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isColorAccessor' does not exist on type ... Remove this comment to see the full error message
isColorAccessor,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isUserDefined' does not exist on type 'R... Remove this comment to see the full error message
isUserDefined,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isGeneSetSummary' does not exist on type... Remove this comment to see the full error message
isGeneSetSummary,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isScatterplotXXaccessor' does not exist ... Remove this comment to see the full error message
isScatterplotXXaccessor,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isScatterplotYYaccessor' does not exist ... Remove this comment to see the full error message
isScatterplotYYaccessor,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'zebra' does not exist on type 'Readonly<... Remove this comment to see the full error message
zebra,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'continuousSelectionRange' does not exist... Remove this comment to see the full error message
continuousSelectionRange,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isObs' does not exist on type 'Readonly<... Remove this comment to see the full error message
isObs,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'mini' does not exist on type 'Readonly<{... Remove this comment to see the full error message
mini,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'setGenes' does not exist on type 'Readon... Remove this comment to see the full error message
setGenes,
} = this.props;
// @ts-expect-error ts-migrate(2339) FIXME: Property 'width' does not exist on type 'Readonly<... Remove this comment to see the full error message
let { width } = this.props;
if (!width) {
width = mini ? WIDTH_MINI : WIDTH;
@@ -392,7 +425,7 @@ class HistogramBrush extends React.PureComponent {
</Async.Rejected>
<Async.Fulfilled>
{(asyncProps) =>
asyncProps.OK2Render ? (
(asyncProps as any).OK2Render ? (
<div
id={`histogram_${fieldForId}`}
data-testid={`histogram-${field}`}
@@ -404,6 +437,7 @@ class HistogramBrush extends React.PureComponent {
>
{!mini && isObs ? (
<HistogramHeader
// @ts-expect-error ts-migrate(2322) FIXME: Type '{ fieldId: any; isColorBy: any; isObs: any; ... Remove this comment to see the full error message
fieldId={field}
isColorBy={isColorAccessor}
isObs={isObs}
@@ -422,9 +456,11 @@ class HistogramBrush extends React.PureComponent {
<Histogram
field={field}
fieldForId={fieldForId}
display={asyncProps.isSingleValue ? "none" : "block"}
display={(asyncProps as any).isSingleValue ? "none" : "block"}
histogram={
mini ? asyncProps.miniHistogram : asyncProps.histogram
mini
? (asyncProps as any).miniHistogram
: (asyncProps as any).histogram
}
width={width}
height={mini ? HEIGHT_MINI : HEIGHT}
@@ -437,14 +473,15 @@ class HistogramBrush extends React.PureComponent {
/>
{!mini && (
<HistogramFooter
// @ts-expect-error ts-migrate(2322) FIXME: Type '{ isGeneSetSummary: any; isObs: any; display... Remove this comment to see the full error message
isGeneSetSummary={isGeneSetSummary}
isObs={isObs}
displayName={field}
hideRanges={asyncProps.isSingleValue}
rangeMin={asyncProps.unclippedRange[0]}
rangeMax={asyncProps.unclippedRange[1]}
rangeColorMin={asyncProps.unclippedRangeColor[0]}
rangeColorMax={asyncProps.unclippedRangeColor[1]}
hideRanges={(asyncProps as any).isSingleValue}
rangeMin={(asyncProps as any).unclippedRange[0]}
rangeMax={(asyncProps as any).unclippedRange[1]}
rangeColorMin={(asyncProps as any).unclippedRangeColor[0]}
rangeColorMax={(asyncProps as any).unclippedRangeColor[1]}
/>
)}
</div>
client/src/components/brushableHistogram/loading.js → client/src/components/brushableHistogram/loading.tsx
+1 -1
View File
@@ -3,7 +3,7 @@ import { Button } from "@blueprintjs/core";
import * as globals from "../../globals";
const StillLoading = ({ zebra, displayName }) => {
const StillLoading = ({ zebra, displayName }: any) => {
/*
Render a loading indicator for the field.
*/
client/src/components/categorical/annoSelect.js → client/src/components/categorical/annoSelect.tsx
+9 -2
View File
@@ -2,16 +2,21 @@ import React from "react";
import { Button, MenuItem } from "@blueprintjs/core";
import { Select } from "@blueprintjs/select";
class DuplicateCategorySelect extends React.PureComponent {
constructor(props) {
type State = any;
class DuplicateCategorySelect extends React.PureComponent<{}, State> {
constructor(props: {}) {
super(props);
this.state = {};
}
render() {
const {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'allCategoryNames' does not exist on type... Remove this comment to see the full error message
allCategoryNames,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'categoryToDuplicate' does not exist on t... Remove this comment to see the full error message
categoryToDuplicate,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'handleModalDuplicateCategorySelection' d... Remove this comment to see the full error message
handleModalDuplicateCategorySelection,
} = this.props;
return (
@@ -31,7 +36,9 @@ class DuplicateCategorySelect extends React.PureComponent {
<MenuItem
data-testclass="duplicate-category-dropdown-option"
onClick={handleClick}
// @ts-expect-error ts-migrate(2322) FIXME: Type 'unknown' is not assignable to type 'Key | nu... Remove this comment to see the full error message
key={d}
// @ts-expect-error ts-migrate(2322) FIXME: Type 'unknown' is not assignable to type 'ReactNod... Remove this comment to see the full error message
text={d}
/>
);
client/src/components/categorical/category/annoDialogAddLabel.js → client/src/components/categorical/category/annoDialogAddLabel.tsx
+23 -14
View File
@@ -5,20 +5,24 @@ import LabelInput from "../../labelInput";
import { labelPrompt, isLabelErroneous } from "../labelUtil";
import actions from "../../../actions";
type State = any;
// @ts-expect-error ts-migrate(1238) FIXME: Unable to resolve signature of class decorator whe... Remove this comment to see the full error message
@connect((state) => ({
annotations: state.annotations,
schema: state.annoMatrix?.schema,
obsCrossfilter: state.obsCrossfilter,
annotations: (state as any).annotations,
schema: (state as any).annoMatrix?.schema,
obsCrossfilter: (state as any).obsCrossfilter,
}))
class Category extends React.PureComponent {
constructor(props) {
class Category extends React.PureComponent<{}, State> {
constructor(props: {}) {
super(props);
this.state = {
newLabelText: "",
};
}
disableAddNewLabelMode = (e) => {
disableAddNewLabelMode = (e: any) => {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message
const { dispatch } = this.props;
this.setState({
newLabelText: "",
@@ -29,10 +33,11 @@ class Category extends React.PureComponent {
if (e) e.preventDefault();
};
handleAddNewLabelToCategory = (e) => {
handleAddNewLabelToCategory = (e: any) => {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message
const { dispatch, metadataField } = this.props;
const { newLabelText } = this.state;
// @ts-expect-error ts-migrate(2554) FIXME: Expected 1 arguments, but got 0.
this.disableAddNewLabelMode();
dispatch(
actions.annotationCreateLabelInCategory(
@@ -44,10 +49,11 @@ class Category extends React.PureComponent {
e.preventDefault();
};
addLabelAndAssignCells = (e) => {
addLabelAndAssignCells = (e: any) => {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message
const { dispatch, metadataField } = this.props;
const { newLabelText } = this.state;
// @ts-expect-error ts-migrate(2554) FIXME: Expected 1 arguments, but got 0.
this.disableAddNewLabelMode();
dispatch(
actions.annotationCreateLabelInCategory(metadataField, newLabelText, true)
@@ -55,26 +61,28 @@ class Category extends React.PureComponent {
e.preventDefault();
};
labelNameError = (name) => {
labelNameError = (name: any) => {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'metadataField' does not exist on type 'R... Remove this comment to see the full error message
const { metadataField, schema } = this.props;
return isLabelErroneous(name, metadataField, schema);
};
instruction = (label) => {
instruction = (label: any) => {
return labelPrompt(this.labelNameError(label), "New, unique label", ":");
};
handleChangeOrSelect = (label) => {
handleChangeOrSelect = (label: any) => {
this.setState({ newLabelText: label });
};
render() {
const { newLabelText } = this.state;
// @ts-expect-error ts-migrate(2339) FIXME: Property 'metadataField' does not exist on type 'R... Remove this comment to see the full error message
const { metadataField, annotations, obsCrossfilter } = this.props;
return (
<>
<AnnoDialog
// @ts-expect-error ts-migrate(2322) FIXME: Type '{ isActive: any; inputProps: { "data-testid"... Remove this comment to see the full error message
isActive={
annotations.isAddingNewLabel &&
annotations.categoryAddingNewLabel === metadataField
@@ -95,6 +103,7 @@ class Category extends React.PureComponent {
handleCancel={this.disableAddNewLabelMode}
annoInput={
<LabelInput
// @ts-expect-error ts-migrate(2322) FIXME: Type '{ labelSuggestions: null; onChange: (label: ... Remove this comment to see the full error message
labelSuggestions={null}
onChange={this.handleChangeOrSelect}
onSelect={this.handleChangeOrSelect}
client/src/components/categorical/category/annoDialogEditCategoryName.js → client/src/components/categorical/category/annoDialogEditCategoryName.tsx
+28 -21
View File
@@ -7,25 +7,30 @@ import { labelPrompt } from "../labelUtil";
import { AnnotationsHelpers } from "../../../util/stateManager";
import actions from "../../../actions";
type State = any;
// @ts-expect-error ts-migrate(1238) FIXME: Unable to resolve signature of class decorator whe... Remove this comment to see the full error message
@connect((state) => ({
annotations: state.annotations,
schema: state.annoMatrix?.schema,
annotations: (state as any).annotations,
schema: (state as any).annoMatrix?.schema,
}))
class AnnoDialogEditCategoryName extends React.PureComponent {
constructor(props) {
class AnnoDialogEditCategoryName extends React.PureComponent<{}, State> {
constructor(props: {}) {
super(props);
this.state = {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'metadataField' does not exist on type '{... Remove this comment to see the full error message
newCategoryText: props.metadataField,
};
}
handleChangeOrSelect = (name) => {
handleChangeOrSelect = (name: any) => {
this.setState({
newCategoryText: name,
});
};
disableEditCategoryMode = () => {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message
const { dispatch, metadataField } = this.props;
dispatch({
type: "annotation: disable category edit mode",
@@ -33,17 +38,19 @@ class AnnoDialogEditCategoryName extends React.PureComponent {
this.setState({ newCategoryText: metadataField });
};
handleEditCategory = (e) => {
handleEditCategory = (e: any) => {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message
const { dispatch, metadataField } = this.props;
const { newCategoryText } = this.state;
/*
test for uniqueness against *all* annotation names, not just the subset
we render as categorical.
*/
// @ts-expect-error ts-migrate(2339) FIXME: Property 'schema' does not exist on type 'Readonly... Remove this comment to see the full error message
const { schema } = this.props;
const allCategoryNames = schema.annotations.obs.columns.map((c) => c.name);
const allCategoryNames = schema.annotations.obs.columns.map(
(c: any) => c.name
);
if (
(allCategoryNames.indexOf(newCategoryText) > -1 &&
newCategoryText !== metadataField) ||
@@ -51,9 +58,7 @@ class AnnoDialogEditCategoryName extends React.PureComponent {
) {
return;
}
this.disableEditCategoryMode();
if (metadataField !== newCategoryText)
dispatch(
actions.annotationRenameCategoryAction(metadataField, newCategoryText)
@@ -61,35 +66,34 @@ class AnnoDialogEditCategoryName extends React.PureComponent {
e.preventDefault();
};
editedCategoryNameError = (name) => {
editedCategoryNameError = (name: any) => {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'metadataField' does not exist on type 'R... Remove this comment to see the full error message
const { metadataField } = this.props;
/* check for syntax errors in category name */
const error = AnnotationsHelpers.annotationNameIsErroneous(name);
if (error) {
return error;
}
/* check for duplicative categories */
/*
test for uniqueness against *all* annotation names, not just the subset
we render as categorical.
*/
// @ts-expect-error ts-migrate(2339) FIXME: Property 'schema' does not exist on type 'Readonly... Remove this comment to see the full error message
const { schema } = this.props;
const allCategoryNames = schema.annotations.obs.columns.map((c) => c.name);
const allCategoryNames = schema.annotations.obs.columns.map(
(c: any) => c.name
);
const categoryNameAlreadyExists = allCategoryNames.indexOf(name) > -1;
const sameName = name === metadataField;
if (categoryNameAlreadyExists && !sameName) {
return "duplicate";
}
/* otherwise, no error */
return false;
};
instruction = (name) => {
instruction = (name: any) => {
return labelPrompt(
this.editedCategoryNameError(name),
"New, unique category name",
@@ -98,17 +102,19 @@ class AnnoDialogEditCategoryName extends React.PureComponent {
};
allCategoryNames() {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'schema' does not exist on type 'Readonly... Remove this comment to see the full error message
const { schema } = this.props;
return schema.annotations.obs.columns.map((c) => c.name);
return schema.annotations.obs.columns.map((c: any) => c.name);
}
render() {
const { newCategoryText } = this.state;
// @ts-expect-error ts-migrate(2339) FIXME: Property 'metadataField' does not exist on type 'R... Remove this comment to see the full error message
const { metadataField, annotations } = this.props;
return (
<>
<AnnoDialog
// @ts-expect-error ts-migrate(2322) FIXME: Type '{ isActive: any; inputProps: { "data-testid"... Remove this comment to see the full error message
isActive={
annotations.isEditingCategoryName &&
annotations.categoryBeingEdited === metadataField
@@ -129,6 +135,7 @@ class AnnoDialogEditCategoryName extends React.PureComponent {
handleCancel={this.disableEditCategoryMode}
annoInput={
<LabelInput
// @ts-expect-error ts-migrate(2322) FIXME: Type '{ label: any; labelSuggestions: null; onChan... Remove this comment to see the full error message
label={newCategoryText}
labelSuggestions={null}
onChange={this.handleChangeOrSelect}
client/src/components/categorical/category/annoMenuCategory.js → client/src/components/categorical/category/annoMenuCategory.tsx
+15 -5
View File
@@ -16,16 +16,20 @@ import { IconNames } from "@blueprintjs/icons";
import * as globals from "../../../globals";
import actions from "../../../actions";
type State = any;
// @ts-expect-error ts-migrate(1238) FIXME: Unable to resolve signature of class decorator whe... Remove this comment to see the full error message
@connect((state) => ({
annotations: state.annotations,
annotations: (state as any).annotations,
}))
class AnnoMenuCategory extends React.PureComponent {
constructor(props) {
class AnnoMenuCategory extends React.PureComponent<{}, State> {
constructor(props: {}) {
super(props);
this.state = {};
}
activateAddNewLabelMode = () => {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message
const { dispatch, metadataField } = this.props;
dispatch({
type: "annotation: activate add new label mode",
@@ -34,8 +38,8 @@ class AnnoMenuCategory extends React.PureComponent {
};
activateEditCategoryMode = () => {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message
const { dispatch, metadataField } = this.props;
dispatch({
type: "annotation: activate category edit mode",
data: metadataField,
@@ -43,20 +47,26 @@ class AnnoMenuCategory extends React.PureComponent {
};
handleDeleteCategory = () => {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message
const { dispatch, metadataField } = this.props;
dispatch(actions.annotationDeleteCategoryAction(metadataField));
};
render() {
const {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'metadataField' does not exist on type 'R... Remove this comment to see the full error message
metadataField,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'annotations' does not exist on type 'Rea... Remove this comment to see the full error message
annotations,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isUserAnno' does not exist on type 'Read... Remove this comment to see the full error message
isUserAnno,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'createText' does not exist on type 'Read... Remove this comment to see the full error message
createText,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'editText' does not exist on type 'Readon... Remove this comment to see the full error message
editText,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'deleteText' does not exist on type 'Read... Remove this comment to see the full error message
deleteText,
} = this.props;
return (
<>
{isUserAnno ? (
client/src/components/categorical/category/index.js → client/src/components/categorical/category/index.tsx
+97 -24
View File
@@ -31,33 +31,39 @@ const LABEL_WIDTH = globals.leftSidebarWidth - 100;
const ANNO_BUTTON_WIDTH = 50;
const LABEL_WIDTH_ANNO = LABEL_WIDTH - ANNO_BUTTON_WIDTH;
// @ts-expect-error ts-migrate(1238) FIXME: Unable to resolve signature of class decorator whe... Remove this comment to see the full error message
@connect((state, ownProps) => {
const schema = state.annoMatrix?.schema;
const schema = (state as any).annoMatrix?.schema;
// @ts-expect-error ts-migrate(2339) FIXME: Property 'metadataField' does not exist on type '{... Remove this comment to see the full error message
const { metadataField } = ownProps;
const isUserAnno = schema?.annotations?.obsByName[metadataField]?.writable;
const categoricalSelection = state.categoricalSelection?.[metadataField];
const categoricalSelection = (state as any).categoricalSelection?.[
metadataField
];
return {
colors: state.colors,
colors: (state as any).colors,
categoricalSelection,
annotations: state.annotations,
annoMatrix: state.annoMatrix,
annotations: (state as any).annotations,
annoMatrix: (state as any).annoMatrix,
schema,
crossfilter: state.obsCrossfilter,
crossfilter: (state as any).obsCrossfilter,
isUserAnno,
genesets: state.genesets.genesets,
genesets: (state as any).genesets.genesets,
};
})
class Category extends React.PureComponent {
static getSelectionState(
categoricalSelection,
metadataField,
categorySummary
categoricalSelection: any,
// @ts-expect-error ts-migrate(6133) FIXME: 'metadataField' is declared but its value is never... Remove this comment to see the full error message
metadataField: any,
categorySummary: any
) {
// total number of categories in this dimension
const totalCatCount = categorySummary.numCategoryValues;
// number of selected options in this category
const selectedCatCount = categorySummary.categoryValues.reduce(
(res, label) => (categoricalSelection.get(label) ?? true ? res + 1 : res),
(res: any, label: any) =>
categoricalSelection.get(label) ?? true ? res + 1 : res,
0
);
return selectedCatCount === totalCatCount
@@ -67,13 +73,14 @@ class Category extends React.PureComponent {
: "some";
}
static watchAsync(props, prevProps) {
static watchAsync(props: any, prevProps: any) {
return !shallowEqual(props.watchProps, prevProps.watchProps);
}
createCategorySummaryFromDfCol = memoize(createCategorySummaryFromDfCol);
getSelectionState(categorySummary) {
getSelectionState(categorySummary: any) {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'categoricalSelection' does not exist on ... Remove this comment to see the full error message
const { categoricalSelection, metadataField } = this.props;
return Category.getSelectionState(
categoricalSelection,
@@ -83,6 +90,7 @@ class Category extends React.PureComponent {
}
handleColorChange = () => {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message
const { dispatch, metadataField } = this.props;
dispatch({
type: "color by categorical metadata",
@@ -91,6 +99,7 @@ class Category extends React.PureComponent {
};
handleCategoryClick = () => {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'annotations' does not exist on type 'Rea... Remove this comment to see the full error message
const { annotations, metadataField, onExpansionChange } = this.props;
const editingCategory =
annotations.isEditingCategoryName &&
@@ -100,13 +109,13 @@ class Category extends React.PureComponent {
}
};
handleCategoryKeyPress = (e) => {
handleCategoryKeyPress = (e: any) => {
if (e.key === "Enter") {
this.handleCategoryClick();
}
};
handleToggleAllClick = (categorySummary) => {
handleToggleAllClick = (categorySummary: any) => {
const isChecked = this.getSelectionState(categorySummary);
if (isChecked === "all") {
this.toggleNone(categorySummary);
@@ -115,8 +124,9 @@ class Category extends React.PureComponent {
}
};
fetchAsyncProps = async (props) => {
fetchAsyncProps = async (props: any) => {
const { annoMatrix, metadataField, colors } = props.watchProps;
// @ts-expect-error ts-migrate(2339) FIXME: Property 'crossfilter' does not exist on type 'Rea... Remove this comment to see the full error message
const { crossfilter } = this.props;
const [categoryData, categorySummary, colorData] = await this.fetchData(
@@ -136,13 +146,14 @@ class Category extends React.PureComponent {
};
};
async fetchData(annoMatrix, metadataField, colors) {
async fetchData(annoMatrix: any, metadataField: any, colors: any) {
/*
fetch our data and the color-by data if appropriate, and then build a summary
of our category and a color table for the color-by annotation.
*/
const { schema } = annoMatrix;
const { colorAccessor, colorMode } = colors;
// @ts-expect-error ts-migrate(2339) FIXME: Property 'genesets' does not exist on type 'Readon... Remove this comment to see the full error message
const { genesets } = this.props;
let colorDataPromise = Promise.resolve(null);
if (colorAccessor) {
@@ -169,8 +180,9 @@ class Category extends React.PureComponent {
return [categoryData, categorySummary, colorData];
}
updateColorTable(colorData) {
updateColorTable(colorData: any) {
// color table, which may be null
// @ts-expect-error ts-migrate(2339) FIXME: Property 'schema' does not exist on type 'Readonly... Remove this comment to see the full error message
const { schema, colors, metadataField } = this.props;
const { colorAccessor, userColors, colorMode } = colors;
return {
@@ -187,7 +199,8 @@ class Category extends React.PureComponent {
};
}
toggleNone(categorySummary) {
toggleNone(categorySummary: any) {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message
const { dispatch, metadataField } = this.props;
dispatch(
actions.selectCategoricalAllMetadataAction(
@@ -199,7 +212,8 @@ class Category extends React.PureComponent {
);
}
toggleAll(categorySummary) {
toggleAll(categorySummary: any) {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message
const { dispatch, metadataField } = this.props;
dispatch(
actions.selectCategoricalAllMetadataAction(
@@ -213,12 +227,19 @@ class Category extends React.PureComponent {
render() {
const {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'metadataField' does not exist on type 'R... Remove this comment to see the full error message
metadataField,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isExpanded' does not exist on type 'Read... Remove this comment to see the full error message
isExpanded,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'categoricalSelection' does not exist on ... Remove this comment to see the full error message
categoricalSelection,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'crossfilter' does not exist on type 'Rea... Remove this comment to see the full error message
crossfilter,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'colors' does not exist on type 'Readonly... Remove this comment to see the full error message
colors,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'annoMatrix' does not exist on type 'Read... Remove this comment to see the full error message
annoMatrix,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isUserAnno' does not exist on type 'Read... Remove this comment to see the full error message
isUserAnno,
} = this.props;
@@ -250,18 +271,26 @@ class Category extends React.PureComponent {
<Async.Fulfilled persist>
{(asyncProps) => {
const {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'colorAccessor' does not exist on type 'u... Remove this comment to see the full error message
colorAccessor,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'colorTable' does not exist on type 'unkn... Remove this comment to see the full error message
colorTable,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'colorData' does not exist on type 'unkno... Remove this comment to see the full error message
colorData,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'categoryData' does not exist on type 'un... Remove this comment to see the full error message
categoryData,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'categorySummary' does not exist on type ... Remove this comment to see the full error message
categorySummary,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isColorAccessor' does not exist on type ... Remove this comment to see the full error message
isColorAccessor,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'handleCategoryToggleAllClick' does not e... Remove this comment to see the full error message
handleCategoryToggleAllClick,
} = asyncProps;
const isTruncated = !!categorySummary?.isTruncated;
const selectionState = this.getSelectionState(categorySummary);
return (
<CategoryRender
// @ts-expect-error ts-migrate(2322) FIXME: Type '{ metadataField: any; checkboxID: string; is... Remove this comment to see the full error message
metadataField={metadataField}
checkboxID={checkboxID}
isUserAnno={isUserAnno}
@@ -290,7 +319,7 @@ class Category extends React.PureComponent {
export default Category;
const StillLoading = ({ metadataField, checkboxID }) => {
const StillLoading = ({ metadataField, checkboxID }: any) => {
/*
We are still loading this category, so render a "busy" signal.
*/
@@ -341,7 +370,7 @@ const StillLoading = ({ metadataField, checkboxID }) => {
);
};
const ErrorLoading = ({ metadataField, error }) => {
const ErrorLoading = ({ metadataField, error }: any) => {
console.error(error); // log error to console as it is unexpected.
return (
<div style={{ marginBottom: 10, marginTop: 4 }}>
@@ -361,16 +390,27 @@ const ErrorLoading = ({ metadataField, error }) => {
const CategoryHeader = React.memo(
({
// @ts-expect-error ts-migrate(2339) FIXME: Property 'metadataField' does not exist on type '{... Remove this comment to see the full error message
metadataField,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'checkboxID' does not exist on type '{ ch... Remove this comment to see the full error message
checkboxID,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isUserAnno' does not exist on type '{ ch... Remove this comment to see the full error message
isUserAnno,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isTruncated' does not exist on type '{ c... Remove this comment to see the full error message
isTruncated,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isColorAccessor' does not exist on type ... Remove this comment to see the full error message
isColorAccessor,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isExpanded' does not exist on type '{ ch... Remove this comment to see the full error message
isExpanded,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'selectionState' does not exist on type '... Remove this comment to see the full error message
selectionState,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'onColorChangeClick' does not exist on ty... Remove this comment to see the full error message
onColorChangeClick,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'onCategoryMenuClick' does not exist on t... Remove this comment to see the full error message
onCategoryMenuClick,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'onCategoryMenuKeyPress' does not exist o... Remove this comment to see the full error message
onCategoryMenuKeyPress,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'onCategoryToggleAllClick' does not exist... Remove this comment to see the full error message
onCategoryToggleAllClick,
}) => {
/*
@@ -379,6 +419,7 @@ const CategoryHeader = React.memo(
const checkboxRef = useRef(null);
useEffect(() => {
// @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
checkboxRef.current.indeterminate = selectionState === "some";
}, [checkboxRef.current, selectionState]);
@@ -408,6 +449,7 @@ const CategoryHeader = React.memo(
</label>
<span
role="menuitem"
// @ts-expect-error ts-migrate(2322) FIXME: Type 'string' is not assignable to type 'number | ... Remove this comment to see the full error message
tabIndex="0"
data-testclass="category-expand"
data-testid={`${metadataField}:category-expand`}
@@ -423,6 +465,7 @@ const CategoryHeader = React.memo(
maxWidth: isUserAnno ? LABEL_WIDTH_ANNO : LABEL_WIDTH,
}}
data-testid={`${metadataField}:category-label`}
// @ts-expect-error ts-migrate(2322) FIXME: Type 'string' is not assignable to type 'number | ... Remove this comment to see the full error message
tabIndex="-1"
>
{metadataField}
@@ -441,10 +484,13 @@ const CategoryHeader = React.memo(
)}
</span>
</div>
{<AnnoDialogEditCategoryName metadataField={metadataField} />}
{<AnnoDialogAddLabel metadataField={metadataField} />}
{/* @ts-expect-error ts-migrate(2322) FIXME: Type '{ metadataField: any; }' is not assignable t... Remove this comment to see the full error message */}
<AnnoDialogEditCategoryName metadataField={metadataField} />
{/* @ts-expect-error ts-migrate(2322) FIXME: Type '{ metadataField: any; }' is not assignable t... Remove this comment to see the full error message */}
<AnnoDialogAddLabel metadataField={metadataField} />
<div>
<AnnoMenu
// @ts-expect-error ts-migrate(2322) FIXME: Type '{ metadataField: any; isUserAnno: any; creat... Remove this comment to see the full error message
metadataField={metadataField}
isUserAnno={isUserAnno}
createText="Add a new label to this category"
@@ -484,21 +530,37 @@ const CategoryHeader = React.memo(
const CategoryRender = React.memo(
({
// @ts-expect-error ts-migrate(2339) FIXME: Property 'metadataField' does not exist on type '{... Remove this comment to see the full error message
metadataField,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'checkboxID' does not exist on type '{ ch... Remove this comment to see the full error message
checkboxID,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isUserAnno' does not exist on type '{ ch... Remove this comment to see the full error message
isUserAnno,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isTruncated' does not exist on type '{ c... Remove this comment to see the full error message
isTruncated,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isColorAccessor' does not exist on type ... Remove this comment to see the full error message
isColorAccessor,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isExpanded' does not exist on type '{ ch... Remove this comment to see the full error message
isExpanded,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'selectionState' does not exist on type '... Remove this comment to see the full error message
selectionState,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'categoryData' does not exist on type '{ ... Remove this comment to see the full error message
categoryData,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'categorySummary' does not exist on type ... Remove this comment to see the full error message
categorySummary,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'colorAccessor' does not exist on type '{... Remove this comment to see the full error message
colorAccessor,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'colorData' does not exist on type '{ chi... Remove this comment to see the full error message
colorData,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'colorTable' does not exist on type '{ ch... Remove this comment to see the full error message
colorTable,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'onColorChangeClick' does not exist on ty... Remove this comment to see the full error message
onColorChangeClick,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'onCategoryMenuClick' does not exist on t... Remove this comment to see the full error message
onCategoryMenuClick,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'onCategoryMenuKeyPress' does not exist o... Remove this comment to see the full error message
onCategoryMenuKeyPress,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'onCategoryToggleAllClick' does not exist... Remove this comment to see the full error message
onCategoryToggleAllClick,
}) => {
/*
@@ -533,6 +595,7 @@ const CategoryRender = React.memo(
}}
>
<CategoryHeader
// @ts-expect-error ts-migrate(2322) FIXME: Type '{ metadataField: any; checkboxID: any; isUse... Remove this comment to see the full error message
metadataField={metadataField}
checkboxID={checkboxID}
isUserAnno={isUserAnno}
@@ -551,6 +614,7 @@ const CategoryRender = React.memo(
/* values*/
isExpanded ? (
<CategoryValueList
// @ts-expect-error ts-migrate(2322) FIXME: Type '{ isUserAnno: any; metadataField: any; categ... Remove this comment to see the full error message
isUserAnno={isUserAnno}
metadataField={metadataField}
categoryData={categoryData}
@@ -574,12 +638,19 @@ const CategoryRender = React.memo(
const CategoryValueList = React.memo(
({
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isUserAnno' does not exist on type '{ ch... Remove this comment to see the full error message
isUserAnno,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'metadataField' does not exist on type '{... Remove this comment to see the full error message
metadataField,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'categoryData' does not exist on type '{ ... Remove this comment to see the full error message
categoryData,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'categorySummary' does not exist on type ... Remove this comment to see the full error message
categorySummary,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'colorAccessor' does not exist on type '{... Remove this comment to see the full error message
colorAccessor,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'colorData' does not exist on type '{ chi... Remove this comment to see the full error message
colorData,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'colorTable' does not exist on type '{ ch... Remove this comment to see the full error message
colorTable,
}) => {
const tuples = [...categorySummary.categoryValueIndices];
@@ -594,6 +665,7 @@ const CategoryValueList = React.memo(
{tuples.map(([value, index]) => (
<Value
key={value}
// @ts-expect-error ts-migrate(2322) FIXME: Type '{ key: any; isUserAnno: any; metadataField: ... Remove this comment to see the full error message
isUserAnno={isUserAnno}
metadataField={metadataField}
categoryIndex={index}
@@ -615,6 +687,7 @@ const CategoryValueList = React.memo(
{tuples.map(([value, index]) => (
<Flipped key={value} flipId={value}>
<Value
// @ts-expect-error ts-migrate(2322) FIXME: Type '{ isUserAnno: any; metadataField: any; categ... Remove this comment to see the full error message
isUserAnno={isUserAnno}
metadataField={metadataField}
categoryIndex={index}
client/src/components/categorical/categoryContext.js → client/src/components/categorical/categoryContext.ts
View File
client/src/components/categorical/index.js → client/src/components/categorical/index.tsx
+31 -26
View File
@@ -10,13 +10,17 @@ import LabelInput from "../labelInput";
import { labelPrompt } from "./labelUtil";
import actions from "../../actions";
type State = any;
// @ts-expect-error ts-migrate(1238) FIXME: Unable to resolve signature of class decorator whe... Remove this comment to see the full error message
@connect((state) => ({
writableCategoriesEnabled: state.config?.parameters?.annotations ?? false,
schema: state.annoMatrix?.schema,
userInfo: state.userInfo,
writableCategoriesEnabled:
(state as any).config?.parameters?.annotations ?? false,
schema: (state as any).annoMatrix?.schema,
userInfo: (state as any).userInfo,
}))
class Categories extends React.Component {
constructor(props) {
class Categories extends React.Component<{}, State> {
constructor(props: {}) {
super(props);
this.state = {
createAnnoModeActive: false,
@@ -26,7 +30,8 @@ class Categories extends React.Component {
};
}
handleCreateUserAnno = (e) => {
handleCreateUserAnno = (e: any) => {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message
const { dispatch } = this.props;
const { newCategoryText, categoryToDuplicate } = this.state;
dispatch(
@@ -55,50 +60,48 @@ class Categories extends React.Component {
});
};
handleModalDuplicateCategorySelection = (d) => {
handleModalDuplicateCategorySelection = (d: any) => {
this.setState({ categoryToDuplicate: d });
};
categoryNameError = (name) => {
categoryNameError = (name: any) => {
/*
return false if this is a LEGAL/acceptable category name or NULL/empty string,
or return an error type.
*/
/* allow empty string */
if (name === "") return false;
/*
test for uniqueness against *all* annotation names, not just the subset
we render as categorical.
*/
// @ts-expect-error ts-migrate(2339) FIXME: Property 'schema' does not exist on type 'Readonly... Remove this comment to see the full error message
const { schema } = this.props;
const allCategoryNames = schema.annotations.obs.columns.map((c) => c.name);
const allCategoryNames = schema.annotations.obs.columns.map(
(c: any) => c.name
);
/* check category name syntax */
const error = AnnotationsHelpers.annotationNameIsErroneous(name);
if (error) {
return error;
}
/* disallow duplicates */
if (allCategoryNames.indexOf(name) !== -1) {
return "duplicate";
}
/* otherwise, no error */
return false;
};
handleChange = (name) => {
handleChange = (name: any) => {
this.setState({ newCategoryText: name });
};
handleSelect = (name) => {
handleSelect = (name: any) => {
this.setState({ newCategoryText: name });
};
instruction = (name) => {
instruction = (name: any) => {
return labelPrompt(
this.categoryNameError(name),
"New, unique category name",
@@ -106,7 +109,7 @@ class Categories extends React.Component {
);
};
onExpansionChange = (catName) => {
onExpansionChange = (catName: any) => {
const { expandedCats } = this.state;
if (expandedCats.has(catName)) {
const _expandedCats = new Set(expandedCats);
@@ -126,16 +129,13 @@ class Categories extends React.Component {
newCategoryText,
expandedCats,
} = this.state;
const {
writableCategoriesEnabled,
schema,
userInfo,
} = this.props;
// @ts-expect-error ts-migrate(2339) FIXME: Property 'writableCategoriesEnabled' does not exis... Remove this comment to see the full error message
const { writableCategoriesEnabled, schema, userInfo } = this.props;
/* all names, sorted in display order. Will be rendered in this order */
// @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1.
const allCategoryNames = ControlsHelpers.selectableCategoryNames(
schema
).sort();
return (
<div
style={{
@@ -143,6 +143,7 @@ class Categories extends React.Component {
}}
>
<AnnoDialog
// @ts-expect-error ts-migrate(2322) FIXME: Type '{ isActive: any; title: string; instruction:... Remove this comment to see the full error message
isActive={createAnnoModeActive}
title="Create new category"
instruction={this.instruction(newCategoryText)}
@@ -155,6 +156,7 @@ class Categories extends React.Component {
handleCancel={this.handleDisableAnnoMode}
annoInput={
<LabelInput
// @ts-expect-error ts-migrate(2322) FIXME: Type '{ labelSuggestions: null; onChange: (name: a... Remove this comment to see the full error message
labelSuggestions={null}
onChange={this.handleChange}
onSelect={this.handleSelect}
@@ -169,6 +171,7 @@ class Categories extends React.Component {
}
annoSelect={
<AnnoSelect
// @ts-expect-error ts-migrate(2322) FIXME: Type '{ handleModalDuplicateCategorySelection: (d:... Remove this comment to see the full error message
handleModalDuplicateCategorySelection={
this.handleModalDuplicateCategorySelection
}
@@ -209,12 +212,13 @@ class Categories extends React.Component {
{/* READ ONLY CATEGORICAL FIELDS */}
{/* this is duplicative but flat, could be abstracted */}
{allCategoryNames.map((catName) =>
{allCategoryNames.map((catName: any) =>
!schema.annotations.obsByName[catName].writable &&
(schema.annotations.obsByName[catName].categories?.length > 1 ||
!schema.annotations.obsByName[catName].categories) ? (
<Category
key={catName}
// @ts-expect-error ts-migrate(2769) FIXME: No overload matches this call.
metadataField={catName}
onExpansionChange={this.onExpansionChange}
isExpanded={expandedCats.has(catName)}
@@ -223,10 +227,11 @@ class Categories extends React.Component {
) : null
)}
{/* WRITEABLE FIELDS */}
{allCategoryNames.map((catName) =>
{allCategoryNames.map((catName: any) =>
schema.annotations.obsByName[catName].writable ? (
<Category
key={catName}
// @ts-expect-error ts-migrate(2769) FIXME: No overload matches this call.
metadataField={catName}
onExpansionChange={this.onExpansionChange}
isExpanded={expandedCats.has(catName)}
client/src/components/categorical/labelUtil.js → client/src/components/categorical/labelUtil.tsx
+3 -2
View File
@@ -3,7 +3,7 @@ import { Colors } from "@blueprintjs/core";
import { AnnotationsHelpers } from "../../util/stateManager";
export function isLabelErroneous(label, metadataField, schema) {
export function isLabelErroneous(label: any, metadataField: any, schema: any) {
/*
return false if this is a LEGAL/acceptable category name or NULL/empty string,
or return an error type.
@@ -35,9 +35,10 @@ const errorMessageMap = {
"multi-space-run": "Multiple consecutive spaces not allowed",
};
export function labelPrompt(err, prolog, epilog) {
export function labelPrompt(err: any, prolog: any, epilog: any) {
let errPrompt = null;
if (err) {
// @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message
let errMsg = errorMessageMap[err] ?? "error";
errMsg = errMsg[0].toLowerCase() + errMsg.slice(1);
errPrompt = (
client/src/components/categorical/value/index.js → client/src/components/categorical/value/index.tsx
+96 -36
View File
@@ -13,6 +13,7 @@ import {
Position,
} from "@blueprintjs/core";
import * as globals from "../../../globals";
// @ts-expect-error ts-migrate(2307) FIXME: Cannot find module '../categorical.css' or its cor... Remove this comment to see the full error message
import styles from "../categorical.css";
import AnnoDialog from "../../annoDialog";
import LabelInput from "../../labelInput";
@@ -29,15 +30,20 @@ const STACKED_BAR_HEIGHT = 11;
const STACKED_BAR_WIDTH = 100;
/* this is defined outside of the class so we can use it in connect() */
function _currentLabelAsString(ownProps) {
function _currentLabelAsString(ownProps: any) {
const { label } = ownProps;
// when called as a function, the String() constructor performs type conversion,
// and returns a primitive string.
return String(label);
}
type State = any;
// @ts-expect-error ts-migrate(1238) FIXME: Unable to resolve signature of class decorator whe... Remove this comment to see the full error message
@connect((state, ownProps) => {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'pointDilation' does not exist on type 'D... Remove this comment to see the full error message
const { pointDilation, categoricalSelection } = state;
// @ts-expect-error ts-migrate(2339) FIXME: Property 'metadataField' does not exist on type '{... Remove this comment to see the full error message
const { metadataField, categorySummary, categoryIndex } = ownProps;
const isDilated =
pointDilation.metadataField === metadataField &&
@@ -48,27 +54,28 @@ function _currentLabelAsString(ownProps) {
const isSelected = category.get(label) ?? true;
return {
annotations: state.annotations,
schema: state.annoMatrix?.schema,
annotations: (state as any).annotations,
schema: (state as any).annoMatrix?.schema,
isDilated,
isSelected,
label,
};
})
class CategoryValue extends React.Component {
constructor(props) {
class CategoryValue extends React.Component<{}, State> {
constructor(props: {}) {
super(props);
this.state = {
editedLabelText: this.currentLabelAsString(),
};
}
componentDidUpdate(prevProps) {
componentDidUpdate(prevProps: {}) {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'metadataField' does not exist on type 'R... Remove this comment to see the full error message
const { metadataField, categoryIndex, categorySummary } = this.props;
if (
prevProps.metadataField !== metadataField ||
prevProps.categoryIndex !== categoryIndex ||
prevProps.categorySummary !== categorySummary
(prevProps as any).metadataField !== metadataField ||
(prevProps as any).categoryIndex !== categoryIndex ||
(prevProps as any).categorySummary !== categorySummary
) {
// eslint-disable-next-line react/no-did-update-set-state --- adequately checked to prevent looping
this.setState({
@@ -79,22 +86,26 @@ class CategoryValue extends React.Component {
// If coloring by and this isn't the colorAccessor and it isn't being edited
get shouldRenderStackedBarOrHistogram() {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'colorAccessor' does not exist on type 'R... Remove this comment to see the full error message
const { colorAccessor, isColorBy, annotations } = this.props;
return !!colorAccessor && !isColorBy && !annotations.isEditingLabelName;
}
handleDeleteValue = () => {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message
const { dispatch, metadataField, label } = this.props;
dispatch(actions.annotationDeleteLabelFromCategory(metadataField, label));
};
handleAddCurrentSelectionToThisLabel = () => {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message
const { dispatch, metadataField, label } = this.props;
dispatch(actions.annotationLabelCurrentSelection(metadataField, label));
};
handleEditValue = (e) => {
handleEditValue = (e: any) => {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message
const { dispatch, metadataField, label } = this.props;
const { editedLabelText } = this.state;
this.cancelEditMode();
@@ -108,7 +119,8 @@ class CategoryValue extends React.Component {
e.preventDefault();
};
handleCreateArbitraryLabel = (txt) => {
handleCreateArbitraryLabel = (txt: any) => {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message
const { dispatch, metadataField, label } = this.props;
this.cancelEditMode();
dispatch(
@@ -116,17 +128,19 @@ class CategoryValue extends React.Component {
);
};
labelNameError = (name) => {
labelNameError = (name: any) => {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'metadataField' does not exist on type 'R... Remove this comment to see the full error message
const { metadataField, schema } = this.props;
if (name === this.currentLabelAsString()) return false;
return isLabelErroneous(name, metadataField, schema);
};
instruction = (label) => {
instruction = (label: any) => {
return labelPrompt(this.labelNameError(label), "New, unique label", ":");
};
activateEditLabelMode = () => {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message
const { dispatch, metadataField, categoryIndex, label } = this.props;
dispatch({
type: "annotation: activate edit label mode",
@@ -137,6 +151,7 @@ class CategoryValue extends React.Component {
};
cancelEditMode = () => {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message
const { dispatch, metadataField, categoryIndex, label } = this.props;
this.setState({
editedLabelText: this.currentLabelAsString(),
@@ -151,9 +166,13 @@ class CategoryValue extends React.Component {
toggleOff = () => {
const {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message
dispatch,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'metadataField' does not exist on type 'R... Remove this comment to see the full error message
metadataField,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'categoryIndex' does not exist on type 'R... Remove this comment to see the full error message
categoryIndex,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'categorySummary' does not exist on type ... Remove this comment to see the full error message
categorySummary,
} = this.props;
const label = categorySummary.categoryValues[categoryIndex];
@@ -168,7 +187,7 @@ class CategoryValue extends React.Component {
);
};
shouldComponentUpdate = (nextProps, nextState) => {
shouldComponentUpdate = (nextProps: any, nextState: any) => {
/*
Checks to see if at least one of the following changed:
* world state
@@ -179,6 +198,7 @@ class CategoryValue extends React.Component {
If and only if true, update the component
*/
const { props, state } = this;
// @ts-expect-error ts-migrate(2339) FIXME: Property 'categoryIndex' does not exist on type 'R... Remove this comment to see the full error message
const { categoryIndex, categorySummary, isSelected } = props;
const {
categoryIndex: newCategoryIndex,
@@ -191,10 +211,12 @@ class CategoryValue extends React.Component {
const labelChanged = label !== newLabel;
const valueSelectionChange = isSelected !== newIsSelected;
const colorAccessorChange = props.colorAccessor !== nextProps.colorAccessor;
const annotationsChange = props.annotations !== nextProps.annotations;
const colorAccessorChange =
(props as any).colorAccessor !== nextProps.colorAccessor;
const annotationsChange =
(props as any).annotations !== nextProps.annotations;
const editingLabel = state.editedLabelText !== nextState.editedLabelText;
const dilationChange = props.isDilated !== nextProps.isDilated;
const dilationChange = (props as any).isDilated !== nextProps.isDilated;
const count = categorySummary.categoryValueCounts[categoryIndex];
const newCount = newCategorySummary.categoryValueCounts[newCategoryIndex];
@@ -205,7 +227,7 @@ class CategoryValue extends React.Component {
// if any one changes, but only for the currently colored-by category.
const colorMightHaveChanged =
nextProps.colorAccessor === nextProps.metadataField &&
props.categorySummary !== nextProps.categorySummary;
(props as any).categorySummary !== nextProps.categorySummary;
return (
labelChanged ||
@@ -221,9 +243,13 @@ class CategoryValue extends React.Component {
toggleOn = () => {
const {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message
dispatch,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'metadataField' does not exist on type 'R... Remove this comment to see the full error message
metadataField,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'categoryIndex' does not exist on type 'R... Remove this comment to see the full error message
categoryIndex,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'categorySummary' does not exist on type ... Remove this comment to see the full error message
categorySummary,
} = this.props;
const label = categorySummary.categoryValues[categoryIndex];
@@ -239,6 +265,7 @@ class CategoryValue extends React.Component {
};
handleMouseEnter = () => {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message
const { dispatch, metadataField, categoryIndex, label } = this.props;
dispatch({
type: "category value mouse hover start",
@@ -249,6 +276,7 @@ class CategoryValue extends React.Component {
};
handleMouseExit = () => {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message
const { dispatch, metadataField, categoryIndex, label } = this.props;
dispatch({
type: "category value mouse hover end",
@@ -258,23 +286,24 @@ class CategoryValue extends React.Component {
});
};
handleTextChange = (text) => {
handleTextChange = (text: any) => {
this.setState({ editedLabelText: text });
};
handleChoice = (e) => {
handleChoice = (e: any) => {
/* Blueprint Suggest format */
this.setState({ editedLabelText: e.target });
};
createHistogramBins = (
metadataField,
categoryData,
colorAccessor,
colorData,
categoryValue,
width,
height
metadataField: any,
categoryData: any,
// @ts-expect-error ts-migrate(6133) FIXME: 'colorAccessor' is declared but its value is never... Remove this comment to see the full error message
colorAccessor: any,
colorData: any,
categoryValue: any,
width: any,
height: any
) => {
/*
Knowing that colorScale is based off continuous data,
@@ -309,14 +338,15 @@ class CategoryValue extends React.Component {
};
createStackedGraphBins = (
metadataField,
categoryData,
colorAccessor,
colorData,
categoryValue,
colorTable,
schema,
width
metadataField: any,
categoryData: any,
colorAccessor: any,
colorData: any,
categoryValue: any,
// @ts-expect-error ts-migrate(6133) FIXME: 'colorTable' is declared but its value is never re... Remove this comment to see the full error message
colorTable: any,
schema: any,
width: any
) => {
/*
Knowing that the color scale is based off of categorical data,
@@ -357,12 +387,13 @@ class CategoryValue extends React.Component {
return _currentLabelAsString(this.props);
}
isAddCurrentSelectionDisabled(crossfilter, category, value) {
isAddCurrentSelectionDisabled(crossfilter: any, category: any, value: any) {
/*
disable "add current selection to label", if one of the following is true:
1. no cells are selected
2. all currently selected cells already have this label, on this category
*/
// @ts-expect-error ts-migrate(2339) FIXME: Property 'categoryData' does not exist on type 'Re... Remove this comment to see the full error message
const { categoryData } = this.props;
// 1. no cells selected?
@@ -382,12 +413,19 @@ class CategoryValue extends React.Component {
renderMiniStackedBar = () => {
const {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'colorAccessor' does not exist on type 'R... Remove this comment to see the full error message
colorAccessor,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'metadataField' does not exist on type 'R... Remove this comment to see the full error message
metadataField,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'categoryData' does not exist on type 'Re... Remove this comment to see the full error message
categoryData,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'colorData' does not exist on type 'Reado... Remove this comment to see the full error message
colorData,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'colorTable' does not exist on type 'Read... Remove this comment to see the full error message
colorTable,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'schema' does not exist on type 'Readonly... Remove this comment to see the full error message
schema,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'label' does not exist on type 'Readonly<... Remove this comment to see the full error message
label,
} = this.props;
const isColorBy = metadataField === colorAccessor;
@@ -425,6 +463,7 @@ class CategoryValue extends React.Component {
domain,
occupancy,
}}
// @ts-expect-error ts-migrate(2322) FIXME: Type '{ height: number; width: number; colorTable:... Remove this comment to see the full error message
height={STACKED_BAR_HEIGHT}
width={STACKED_BAR_WIDTH}
/>
@@ -433,12 +472,19 @@ class CategoryValue extends React.Component {
renderMiniHistogram = () => {
const {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'colorAccessor' does not exist on type 'R... Remove this comment to see the full error message
colorAccessor,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'metadataField' does not exist on type 'R... Remove this comment to see the full error message
metadataField,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'colorData' does not exist on type 'Reado... Remove this comment to see the full error message
colorData,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'categoryData' does not exist on type 'Re... Remove this comment to see the full error message
categoryData,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'colorTable' does not exist on type 'Read... Remove this comment to see the full error message
colorTable,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'schema' does not exist on type 'Readonly... Remove this comment to see the full error message
schema,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'label' does not exist on type 'Readonly<... Remove this comment to see the full error message
label,
} = this.props;
const colorScale = colorTable?.scale;
@@ -473,6 +519,7 @@ class CategoryValue extends React.Component {
yScale,
bins,
}}
// @ts-expect-error ts-migrate(2322) FIXME: Type '{ obsOrVarContinuousFieldDisplayName: any; d... Remove this comment to see the full error message
obsOrVarContinuousFieldDisplayName={colorAccessor}
domainLabel={label}
height={STACKED_BAR_HEIGHT}
@@ -483,15 +530,25 @@ class CategoryValue extends React.Component {
render() {
const {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'metadataField' does not exist on type 'R... Remove this comment to see the full error message
metadataField,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'categoryIndex' does not exist on type 'R... Remove this comment to see the full error message
categoryIndex,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'colorAccessor' does not exist on type 'R... Remove this comment to see the full error message
colorAccessor,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'colorTable' does not exist on type 'Read... Remove this comment to see the full error message
colorTable,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isUserAnno' does not exist on type 'Read... Remove this comment to see the full error message
isUserAnno,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'annotations' does not exist on type 'Rea... Remove this comment to see the full error message
annotations,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isDilated' does not exist on type 'Reado... Remove this comment to see the full error message
isDilated,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isSelected' does not exist on type 'Read... Remove this comment to see the full error message
isSelected,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'categorySummary' does not exist on type ... Remove this comment to see the full error message
categorySummary,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'label' does not exist on type 'Readonly<... Remove this comment to see the full error message
label,
} = this.props;
const colorScale = colorTable?.scale;
@@ -587,6 +644,7 @@ class CategoryValue extends React.Component {
<span
data-testid={`categorical-value-${metadataField}-${displayString}`}
data-testclass="categorical-value"
// @ts-expect-error ts-migrate(2322) FIXME: Type 'string' is not assignable to type 'number | ... Remove this comment to see the full error message
tabIndex="-1"
style={{
width: labelWidth,
@@ -612,6 +670,7 @@ class CategoryValue extends React.Component {
{editModeActive ? (
<div>
<AnnoDialog
// @ts-expect-error ts-migrate(2322) FIXME: Type '{ isActive: any; inputProps: { "data-testid"... Remove this comment to see the full error message
isActive={editModeActive}
inputProps={{
"data-testid": `${metadataField}:edit-label-name-dialog`,
@@ -630,6 +689,7 @@ class CategoryValue extends React.Component {
handleCancel={this.cancelEditMode}
annoInput={
<LabelInput
// @ts-expect-error ts-migrate(2322) FIXME: Type '{ label: any; labelSuggestions: null; onChan... Remove this comment to see the full error message
label={editedLabelText}
labelSuggestions={null}
onChange={this.handleTextChange}
client/src/components/categorical/value/occupancy.js → client/src/components/categorical/value/occupancy.tsx
+16 -22
View File
@@ -8,10 +8,13 @@ import {
Position,
} from "@blueprintjs/core";
// @ts-expect-error ts-migrate(1238) FIXME: Unable to resolve signature of class decorator whe... Remove this comment to see the full error message
@connect((state) => ({
schema: state.annoMatrix?.schema,
schema: (state as any).annoMatrix?.schema,
}))
class Occupancy extends React.PureComponent {
canvas: any;
_WIDTH = 100;
_HEIGHT = 11;
@@ -23,49 +26,41 @@ class Occupancy extends React.PureComponent {
It then seperates that data into 50 bins for drawing the mini-histogram
*/
const {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'metadataField' does not exist on type 'R... Remove this comment to see the full error message
metadataField,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'categoryData' does not exist on type 'Re... Remove this comment to see the full error message
categoryData,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'colorData' does not exist on type 'Reado... Remove this comment to see the full error message
colorData,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'categoryValue' does not exist on type 'R... Remove this comment to see the full error message
categoryValue,
} = this.props;
if (!this.canvas) return;
const groupBy = categoryData.col(metadataField);
const col = colorData.icol(0);
const range = col.summarize();
const histogramMap = col.histogram(
50,
[range.min, range.max],
groupBy
); /* Because the signature changes we really need different names for histogram to differentiate signatures */
const bins = histogramMap.has(categoryValue)
? histogramMap.get(categoryValue)
: new Array(50).fill(0);
const xScale = d3
.scaleLinear()
.domain([0, bins.length])
.range([0, this._WIDTH]);
const largestBin = Math.max(...bins);
const yScale = d3
.scaleLinear()
.domain([0, largestBin])
.range([0, this._HEIGHT]);
const ctx = this.canvas.getContext("2d");
ctx.fillStyle = "#000";
let x;
let y;
const rectWidth = this._WIDTH / bins.length;
for (let i = 0, { length } = bins; i < length; i += 1) {
x = xScale(i);
y = yScale(bins[i]);
@@ -80,27 +75,29 @@ class Occupancy extends React.PureComponent {
Using the colorScale a stack of colored bars is drawn representing the map
*/
const {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'metadataField' does not exist on type 'R... Remove this comment to see the full error message
metadataField,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'categoryData' does not exist on type 'Re... Remove this comment to see the full error message
categoryData,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'colorAccessor' does not exist on type 'R... Remove this comment to see the full error message
colorAccessor,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'categoryValue' does not exist on type 'R... Remove this comment to see the full error message
categoryValue,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'colorTable' does not exist on type 'Read... Remove this comment to see the full error message
colorTable,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'schema' does not exist on type 'Readonly... Remove this comment to see the full error message
schema,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'colorData' does not exist on type 'Reado... Remove this comment to see the full error message
colorData,
} = this.props;
const { scale: colorScale } = colorTable;
const ctx = this.canvas?.getContext("2d");
if (!ctx) return;
const groupBy = categoryData.col(metadataField);
const occupancyMap = colorData
.col(colorAccessor)
.histogramCategorical(groupBy);
const occupancy = occupancyMap.get(categoryValue);
if (occupancy && occupancy.size > 0) {
// not all categories have occupancy, so occupancy may be undefined.
const x = d3
@@ -110,15 +107,12 @@ class Occupancy extends React.PureComponent {
.range([0, this._WIDTH]);
const categories =
schema.annotations.obsByName[colorAccessor]?.categories;
let currentOffset = 0;
const dfColumn = colorData.col(colorAccessor);
const categoryValues = dfColumn.summarizeCategorical().categories;
let o;
let scaledValue;
let value;
for (let i = 0, { length } = categoryValues; i < length; i += 1) {
value = categoryValues[i];
o = occupancy.get(value);
@@ -133,11 +127,11 @@ class Occupancy extends React.PureComponent {
};
render() {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'colorAccessor' does not exist on type 'R... Remove this comment to see the full error message
const { colorAccessor, categoryValue, colorByIsCategorical } = this.props;
const { canvas } = this;
if (canvas)
canvas.getContext("2d").clearRect(0, 0, this._WIDTH, this._HEIGHT);
return (
<Popover
interactionKind={PopoverInteractionKind.HOVER_TARGET_ONLY}
client/src/components/continuous/continuous.js
-32
View File
@@ -1,32 +0,0 @@
/* rc slider https://www.npmjs.com/package/rc-slider */
import React from "react";
import { connect } from "react-redux";
import HistogramBrush from "../brushableHistogram";
@connect((state) => ({
schema: state.annoMatrix?.schema,
}))
class Continuous extends React.PureComponent {
render() {
/* initial value for iterator to simulate index, ranges is an object */
const { schema } = this.props;
if (!schema) return null;
const obsIndex = schema.annotations.obs.index;
const allContinuousNames = schema.annotations.obs.columns
.filter((col) => col.type === "int32" || col.type === "float32")
.filter((col) => col.name !== obsIndex)
.filter((col) => !col.writable) // skip user annotations - they will be treated as categorical
.map((col) => col.name);
return (
<div>
{allContinuousNames.map((key, zebra) => (
<HistogramBrush key={key} field={key} isObs zebra={zebra % 2 === 0} />
))}
</div>
);
}
}
export default Continuous;
client/src/components/continuous/continuous.tsx
+34
View File
@@ -0,0 +1,34 @@
/* rc slider https://www.npmjs.com/package/rc-slider */
import React from "react";
import { connect } from "react-redux";
import HistogramBrush from "../brushableHistogram";
// @ts-expect-error ts-migrate(1238) FIXME: Unable to resolve signature of class decorator whe... Remove this comment to see the full error message
@connect((state) => ({
schema: (state as any).annoMatrix?.schema,
}))
class Continuous extends React.PureComponent {
render() {
/* initial value for iterator to simulate index, ranges is an object */
// @ts-expect-error ts-migrate(2339) FIXME: Property 'schema' does not exist on type 'Readonly... Remove this comment to see the full error message
const { schema } = this.props;
if (!schema) return null;
const obsIndex = schema.annotations.obs.index;
const allContinuousNames = schema.annotations.obs.columns
.filter((col: any) => col.type === "int32" || col.type === "float32")
.filter((col: any) => col.name !== obsIndex)
.filter((col: any) => !col.writable) // skip user annotations - they will be treated as categorical
.map((col: any) => col.name);
return (
<div>
{allContinuousNames.map((key: any, zebra: any) => (
// @ts-expect-error ts-migrate(2769) FIXME: No overload matches this call.
<HistogramBrush key={key} field={key} isObs zebra={zebra % 2 === 0} />
))}
</div>
);
}
}
export default Continuous;
client/src/components/continuous/setupParallelCoordinates.js → client/src/components/continuous/setupParallelCoordinates.ts
+6 -1
View File
@@ -5,7 +5,7 @@
******************************************/
import * as d3 from "d3";
const setupParallelCoordinates = (width, height, margin) => {
const setupParallelCoordinates = (width: any, height: any, margin: any) => {
const container = d3.select("#parcoords");
const svg = container
@@ -24,10 +24,15 @@ const setupParallelCoordinates = (width, height, margin) => {
.style("margin-top", `${margin.top}px`)
.style("margin-left", `${margin.left}px`);
// @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
const ctx = canvas.node().getContext("2d");
// @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
ctx.globalCompositeOperation = "darken";
// @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
ctx.globalAlpha = 0.15;
// @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
ctx.lineWidth = 1.5;
// @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
ctx.scale(devicePixelRatio, devicePixelRatio);
return {
client/src/components/continuous/util.js → client/src/components/continuous/util.ts
+7 -6
View File
@@ -12,14 +12,14 @@ export const innerHeight = height - 2;
export const devicePixelRatio = window.devicePixelRatio || 1;
export const createDimensions = (data) => {
const newArr = [];
export const createDimensions = (data: any) => {
const newArr: any = [];
each(data, (value, key) => {
if (value.range) {
newArr.push({
key /* room for confusion: lodash calls this key, it's also the name of the property parallel coords code is looking for */,
type: {
within: (d, extent, dim) =>
within: (d: any, extent: any, dim: any) =>
extent[0] <= dim.scale(d) && dim.scale(d) <= extent[1],
},
scale: d3
@@ -32,16 +32,17 @@ export const createDimensions = (data) => {
return newArr;
};
// @ts-expect-error ts-migrate(2554) FIXME: Expected 1 arguments, but got 0.
export const yAxis = d3.axisLeft();
export const brushstart = () => {
d3.event.sourceEvent.stopPropagation();
(d3 as any).event.sourceEvent.stopPropagation();
};
// Unused.
// export const d3_functor = v => (typeof v === "function" ? v : () => v);
export const project = (d, dimensions, xscale) =>
dimensions.map((p, i) => {
export const project = (d: any, dimensions: any, xscale: any) =>
dimensions.map((p: any, i: any) => {
// check if data element has property and contains a value
if (!(p.key in d) || d[p.key] === null) return null;
client/src/components/continuousLegend/index.js → client/src/components/continuousLegend/index.tsx
+13 -11
View File
@@ -9,7 +9,7 @@ import {
} from "../../util/stateManager/colorHelpers";
// create continuous color legend
const continuous = (selectorId, colorScale, colorAccessor) => {
const continuous = (selectorId: any, colorScale: any, colorAccessor: any) => {
const legendHeight = 200;
const legendWidth = 80;
const margin = { top: 10, right: 60, bottom: 10, left: 2 };
@@ -33,6 +33,7 @@ const continuous = (selectorId, colorScale, colorAccessor) => {
we flip the color scale as well [1, 0] instead of [0, 1] */
.node();
// @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
const ctx = canvas.getContext("2d");
const legendScale = d3
@@ -44,6 +45,7 @@ const continuous = (selectorId, colorScale, colorAccessor) => {
]); /* we flip this to make viridis colors dark if high in the color scale */
// image data hackery based on http://bl.ocks.org/mbostock/048d21cf747371b11884f75ad896e5a5
// @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
const image = ctx.createImageData(1, legendHeight);
d3.range(legendHeight).forEach((i) => {
const c = d3.rgb(colorScale(legendScale.invert(i)));
@@ -52,6 +54,7 @@ const continuous = (selectorId, colorScale, colorAccessor) => {
image.data[4 * i + 2] = c.b;
image.data[4 * i + 3] = 255;
});
// @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'.
ctx.putImageData(image, 0, 0);
// A simpler way to do the above, but possibly slower. keep in mind the legend
@@ -105,27 +108,26 @@ const continuous = (selectorId, colorScale, colorAccessor) => {
.text(colorAccessor);
};
// @ts-expect-error ts-migrate(1238) FIXME: Unable to resolve signature of class decorator whe... Remove this comment to see the full error message
@connect((state) => ({
annoMatrix: state.annoMatrix,
colors: state.colors,
genesets: state.genesets.genesets,
annoMatrix: (state as any).annoMatrix,
colors: (state as any).colors,
genesets: (state as any).genesets.genesets,
}))
class ContinuousLegend extends React.Component {
async componentDidUpdate(prevProps) {
async componentDidUpdate(prevProps: any) {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'annoMatrix' does not exist on type 'Read... Remove this comment to see the full error message
const { annoMatrix, colors, genesets } = this.props;
if (!colors || !annoMatrix) return;
if (colors !== prevProps?.colors || annoMatrix !== prevProps?.annoMatrix) {
const { schema } = annoMatrix;
const { colorMode, colorAccessor, userColors } = colors;
const colorQuery = createColorQuery(
colorMode,
colorAccessor,
schema,
genesets
);
const colorDf = colorQuery ? await annoMatrix.fetch(...colorQuery) : null;
const colorTable = createColorTable(
colorMode,
@@ -134,19 +136,19 @@ class ContinuousLegend extends React.Component {
schema,
userColors
);
const colorScale = colorTable.scale;
// @ts-expect-error ts-migrate(2339) FIXME: Property 'range' does not exist on type '((idx: an... Remove this comment to see the full error message
const range = colorScale?.range;
// @ts-expect-error ts-migrate(2339) FIXME: Property 'domain' does not exist on type '((idx: a... Remove this comment to see the full error message
const [domainMin, domainMax] = colorScale?.domain?.() ?? [0, 0];
/* always remove it, if it's not continuous we don't put it back. */
d3.select("#continuous_legend").selectAll("*").remove();
if (colorAccessor && colorScale && range && domainMin < domainMax) {
/* fragile! continuous range is 0 to 1, not [#fa4b2c, ...], make this a flag? */
if (range()[0][0] !== "#") {
continuous(
"#continuous_legend",
// @ts-expect-error ts-migrate(2339) FIXME: Property 'domain' does not exist on type '((idx: a... Remove this comment to see the full error message
d3.scaleSequential(interpolateCool).domain(colorScale.domain()),
colorAccessor
);
client/src/components/embedding/index.js → client/src/components/embedding/index.tsx
+17 -11
View File
@@ -15,25 +15,30 @@ import * as globals from "../../globals";
import actions from "../../actions";
import { getDiscreteCellEmbeddingRowIndex } from "../../util/stateManager/viewStackHelpers";
type EmbeddingState = any;
// @ts-expect-error ts-migrate(1238) FIXME: Unable to resolve signature of class decorator whe... Remove this comment to see the full error message
@connect((state) => {
return {
layoutChoice: state.layoutChoice, // TODO: really should clean up naming, s/layout/embedding/g
schema: state.annoMatrix?.schema,
crossfilter: state.obsCrossfilter,
layoutChoice: (state as any).layoutChoice,
schema: (state as any).annoMatrix?.schema,
crossfilter: (state as any).obsCrossfilter,
};
})
class Embedding extends React.PureComponent {
constructor(props) {
class Embedding extends React.PureComponent<{}, EmbeddingState> {
constructor(props: {}) {
super(props);
this.state = {};
}
handleLayoutChoiceChange = (e) => {
handleLayoutChoiceChange = (e: any) => {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message
const { dispatch } = this.props;
dispatch(actions.layoutChoiceAction(e.currentTarget.value));
};
render() {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'layoutChoice' does not exist on type 'Re... Remove this comment to see the full error message
const { layoutChoice, schema, crossfilter } = this.props;
const { annoMatrix } = crossfilter;
return (
@@ -100,10 +105,11 @@ class Embedding extends React.PureComponent {
export default Embedding;
const loadAllEmbeddingCounts = async ({ annoMatrix, available }) => {
const loadAllEmbeddingCounts = async ({ annoMatrix, available }: any) => {
const embeddings = await Promise.all(
available.map((name) => annoMatrix.base().fetch("emb", name))
available.map((name: any) => annoMatrix.base().fetch("emb", name))
);
// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'name' implicitly has an 'any' type.
return available.map((name, idx) => ({
embeddingName: name,
embedding: embeddings[idx],
@@ -111,7 +117,7 @@ const loadAllEmbeddingCounts = async ({ annoMatrix, available }) => {
}));
};
const EmbeddingChoices = ({ onChange, annoMatrix, layoutChoice }) => {
const EmbeddingChoices = ({ onChange, annoMatrix, layoutChoice }: any) => {
const { available } = layoutChoice;
const { data, error, isPending } = useAsync({
promiseFn: loadAllEmbeddingCounts,
@@ -127,7 +133,7 @@ const EmbeddingChoices = ({ onChange, annoMatrix, layoutChoice }) => {
/* still loading, or errored out - just omit counts (TODO: spinner?) */
return (
<RadioGroup onChange={onChange} selectedValue={layoutChoice.current}>
{layoutChoice.available.map((name) => (
{layoutChoice.available.map((name: any) => (
<Radio label={`${name}`} value={name} key={name} />
))}
</RadioGroup>
@@ -136,7 +142,7 @@ const EmbeddingChoices = ({ onChange, annoMatrix, layoutChoice }) => {
if (data) {
return (
<RadioGroup onChange={onChange} selectedValue={layoutChoice.current}>
{data.map((summary) => {
{data.map((summary: any) => {
const { discreteCellIndex, embeddingName } = summary;
const sizeHint = `${discreteCellIndex.size()} cells`;
return (
client/src/components/framework/container.js → client/src/components/framework/container.tsx
+1 -1
View File
@@ -1,6 +1,6 @@
import React from "react";
function Container(props) {
function Container(props: any) {
const { children } = props;
return (
<div
client/src/components/framework/layout.js → client/src/components/framework/layout.tsx
+2
View File
@@ -2,6 +2,7 @@ import React from "react";
import * as globals from "../../globals";
class Layout extends React.Component {
viewportRef: any;
/*
Layout - this react component contains all the layout style and logic for the application once it has loaded.
@@ -23,6 +24,7 @@ class Layout extends React.Component {
render() {
const { children } = this.props;
// @ts-expect-error ts-migrate(2488) FIXME: Type 'ReactNode' must have a '[Symbol.iterator]()'... Remove this comment to see the full error message
const [leftSidebar, renderGraph, rightSidebar] = children;
return (
<div
client/src/components/framework/logo.js → client/src/components/framework/logo.tsx
+1 -1
View File
@@ -1,7 +1,7 @@
import React from "react";
import * as globals from "../../globals";
const Logo = (props) => {
const Logo = (props: any) => {
const { size } = props;
return (
<svg width={size} height={size} viewBox="0 0 48 48" fill="none">
client/src/components/framework/toasters.js → client/src/components/framework/toasters.ts
+5 -5
View File
@@ -11,20 +11,20 @@ const ToastTopCenter = Toaster.create({
/*
A "user" error - eg, bad input
*/
export const postUserErrorToast = (message) =>
export const postUserErrorToast = (message: any) =>
ToastTopCenter.show({ message, intent: Intent.WARNING });
/*
A toast the user must dismiss manually, because they need to act on its information,
ie., 8 bulk add genes out of 40 were bad. Manually see which ones and fix.
*/
export const keepAroundErrorToast = (message) =>
export const keepAroundErrorToast = (message: any) =>
ToastTopCenter.show({ message, timeout: 0, intent: Intent.WARNING });
/*
a hard network error
*/
export const postNetworkErrorToast = (message, key = undefined) =>
export const postNetworkErrorToast = (message: any, key = undefined) =>
ToastTopCenter.show(
{
message,
@@ -37,14 +37,14 @@ export const postNetworkErrorToast = (message, key = undefined) =>
/*
Async message to user
*/
export const postAsyncSuccessToast = (message) =>
export const postAsyncSuccessToast = (message: any) =>
ToastTopCenter.show({
message,
timeout: 10000,
intent: Intent.SUCCESS,
});
export const postAsyncFailureToast = (message) =>
export const postAsyncFailureToast = (message: any) =>
ToastTopCenter.show({
message,
timeout: 10000,
client/src/components/geneExpression/gene.js → client/src/components/geneExpression/gene.tsx
+25 -5
View File
@@ -9,17 +9,23 @@ import actions from "../../actions";
const MINI_HISTOGRAM_WIDTH = 110;
type State = any;
// @ts-expect-error ts-migrate(1238) FIXME: Unable to resolve signature of class decorator whe... Remove this comment to see the full error message
@connect((state, ownProps) => {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'gene' does not exist on type '{}'.
const { gene } = ownProps;
return {
isColorAccessor: state.colors.colorAccessor === gene,
isScatterplotXXaccessor: state.controls.scatterplotXXaccessor === gene,
isScatterplotYYaccessor: state.controls.scatterplotYYaccessor === gene,
isColorAccessor: (state as any).colors.colorAccessor === gene,
isScatterplotXXaccessor:
(state as any).controls.scatterplotXXaccessor === gene,
isScatterplotYYaccessor:
(state as any).controls.scatterplotYYaccessor === gene,
};
})
class Gene extends React.Component {
constructor(props) {
class Gene extends React.Component<{}, State> {
constructor(props: {}) {
super(props);
this.state = {
geneIsExpanded: false,
@@ -27,6 +33,7 @@ class Gene extends React.Component {
}
onColorChangeClick = () => {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message
const { dispatch, gene } = this.props;
dispatch(actions.requestSingleGeneExpressionCountsForColoringPOST(gene));
};
@@ -37,6 +44,7 @@ class Gene extends React.Component {
};
handleSetGeneAsScatterplotX = () => {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message
const { dispatch, gene } = this.props;
dispatch({
type: "set scatterplot x",
@@ -45,6 +53,7 @@ class Gene extends React.Component {
};
handleSetGeneAsScatterplotY = () => {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message
const { dispatch, gene } = this.props;
dispatch({
type: "set scatterplot y",
@@ -53,18 +62,26 @@ class Gene extends React.Component {
};
handleDeleteGeneFromSet = () => {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message
const { dispatch, gene, geneset } = this.props;
dispatch(actions.genesetDeleteGenes(geneset, [gene]));
};
render() {
const {
// @ts-expect-error ts-migrate(2339) FIXME: Property 'gene' does not exist on type 'Readonly<{... Remove this comment to see the full error message
gene,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'geneDescription' does not exist on type ... Remove this comment to see the full error message
geneDescription,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isColorAccessor' does not exist on type ... Remove this comment to see the full error message
isColorAccessor,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isScatterplotXXaccessor' does not exist ... Remove this comment to see the full error message
isScatterplotXXaccessor,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'isScatterplotYYaccessor' does not exist ... Remove this comment to see the full error message
isScatterplotYYaccessor,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'quickGene' does not exist on type 'Reado... Remove this comment to see the full error message
quickGene,
// @ts-expect-error ts-migrate(2339) FIXME: Property 'removeGene' does not exist on type 'Read... Remove this comment to see the full error message
removeGene,
} = this.props;
const { geneIsExpanded } = this.state;
@@ -84,6 +101,7 @@ class Gene extends React.Component {
>
<div
role="menuitem"
// @ts-expect-error ts-migrate(2322) FIXME: Type 'string' is not assignable to type 'number | ... Remove this comment to see the full error message
tabIndex="0"
data-testclass="gene-expand"
data-testid={`${gene}:gene-expand`}
@@ -124,6 +142,7 @@ class Gene extends React.Component {
</div>
{!geneIsExpanded ? (
<HistogramBrush
// @ts-expect-error ts-migrate(2769) FIXME: No overload matches this call.
isUserDefined
field={gene}
mini
@@ -188,6 +207,7 @@ class Gene extends React.Component {
/>
</div>
</div>
{/* @ts-expect-error ts-migrate(2769) FIXME: No overload matches this call. */}
{geneIsExpanded && <HistogramBrush isUserDefined field={gene} />}
</div>
);

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