chore: updated more linting plugins and fixed sonarjs errors (#4309)

.eslintrc.json

@@ -14,7 +14,7 @@
     "prettier",
     "plugin:prettier/recommended",
     "next",
-    "plugin:sonarjs/recommended",
+    "plugin:sonarjs/recommended-legacy",
     "plugin:eslint-comments/recommended"
   ],
   "rules": {
@@ -57,7 +57,10 @@
     "jsdoc/require-returns-description": "error",
     "jsdoc/check-alignment": "error",
     "jsdoc/check-param-names": "error",
-    "react-hooks/exhaustive-deps": "error"
+    "react-hooks/exhaustive-deps": "error",
+    "sonarjs/todo-tag": "warn",
+    "sonarjs/redundant-type-aliases": "warn",
+    "sonarjs/no-nested-conditional": "warn"
   },
   "overrides": [
     {

__tests__/project-matrix-mapper.test.ts

@@ -25,12 +25,12 @@ const LYMPH_NODE = "lymph node";
 const MOCK_PROJECT_MATRIX_FILE_0 = {
   name: "123.loom",
   size: 254147853,
-  url: "http://path/to/file0?version=0&catalog=dcp2ebi",
+  url: "https://path/to/file0?version=0&catalog=dcp2ebi",
 };
 const MOCK_PROJECT_MATRIX_FILE_1 = {
   name: "456.loom",
   size: 254147854,
-  url: "http://path/to/file1?version=0&catalog=dcp2ebi",
+  url: "https://path/to/file1?version=0&catalog=dcp2ebi",
 };
 const CONTRIBUTED_ANALYSES = {
   genusSpecies: {

app/components/Detail/components/GeneratedMatricesTables/components/FileLocationArchivePreview/fileLocationArchivePreview.tsx

@@ -24,7 +24,7 @@ export const FileLocationArchivePreview = ({
   projectMatrixView,
 }: FileLocationArchivePreviewProps): JSX.Element | null => {
   const [open, setOpen] = useState<boolean>(false);
-  // eslint-disable-next-line @typescript-eslint/no-unused-vars -- TODO future loading state for archive preview dialog.
+  // eslint-disable-next-line @typescript-eslint/no-unused-vars, sonarjs/no-unused-vars, sonarjs/no-dead-store -- TODO future loading state for archive preview dialog.
   const [loading, setLoading] = useState<boolean>(false);
   return isArchivePreviewAvailable(projectMatrixView) ? (
     <>

app/viewModelBuilders/azul/hca-dcp/common/projectMapper/projectEdits/constants.ts

@@ -368,7 +368,7 @@ export const baseProjectEdits: ProjectEdit[] = [
     analysisPortals: [
       {
         ...GENOME_BROWSER,
-        url: "http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&tabulamurisBarChart=pack",
+        url: "https://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&tabulamurisBarChart=pack",
       },
       {
         ...UCSC_CELL_BROWSER,
@@ -672,7 +672,7 @@ export const baseProjectEdits: ProjectEdit[] = [
       },
       {
         ...SHINY,
-        url: "http://devapp.lungmap.net/app/shinycell-lungmap-single-cell-multiomic",
+        url: "https://devapp.lungmap.net/app/shinycell-lungmap-single-cell-multiomic",
       },
       {
         ...TOPPCELL,

app/viewModelBuilders/azul/hca-dcp/common/viewModelBuilders.ts

@@ -22,7 +22,10 @@ import {
 } from "@databiosphere/findable-ui/lib/components/Export/common/entities";
 import { CurrentQuery } from "@databiosphere/findable-ui/lib/components/Export/components/ExportSummary/components/ExportCurrentQuery/exportCurrentQuery";
 import { Summary } from "@databiosphere/findable-ui/lib/components/Export/components/ExportSummary/components/ExportSelectedDataSummary/exportSelectedDataSummary";
-import { ANCHOR_TARGET } from "@databiosphere/findable-ui/lib/components/Links/common/entities";
+import {
+  ANCHOR_TARGET,
+  REL_ATTRIBUTE,
+} from "@databiosphere/findable-ui/lib/components/Links/common/entities";
 import { getConfig } from "@databiosphere/findable-ui/lib/config/config";
 import { ViewContext } from "@databiosphere/findable-ui/lib/config/entities";
 import {
@@ -712,11 +715,14 @@ export const buildCookieBanner = (): React.ComponentProps<
       "This website uses cookies for security and analytics purposes. By using this site, you agree to these uses.",
     secondaryAction: C.ButtonOutline({
       children: "Learn More",
+      /* eslint-disable sonarjs/link-with-target-blank -- const used for NOOPRNER NOREFERRER */
       onClick: () =>
         window.open(
           "https://data.humancellatlas.org/privacy",
-          ANCHOR_TARGET.BLANK
+          ANCHOR_TARGET.BLANK,
+          REL_ATTRIBUTE.NO_OPENER_NO_REFERRER
         ),
+      /* eslint-enable sonarjs/link-with-target-blank -- check target blank links for the rest of the file */
     }),
   };
 };

e2e/anvil/anvil-backpages.spec.ts

@@ -6,6 +6,8 @@ import {
 } from "../testFunctions";
 import { ANVIL_TABS } from "./anvil-tabs";
 
+//TODO: this should probably check a feature flag instead
+//eslint-disable-next-line sonarjs/no-skipped-tests -- disabled since Export to Terra is disabled on AnVIL
 test.skip("Smoke test `Export to Terra` button on the first available dataset", async ({
   context,
   page,
@@ -20,6 +22,8 @@ test.skip("Smoke test `Export to Terra` button on the first available dataset",
   }
 });
 
+//TODO: this should probably check a feature flag instead
+//eslint-disable-next-line sonarjs/no-skipped-tests -- disabled since Export to Terra is disabled on AnVIL
 test.skip("Check access controls on the datasets backpages work for the first two tabs", async ({
   page,
 }) => {

e2e/anvil/anvil-filters.spec.ts

@@ -65,7 +65,7 @@ test("Check that all filters exist on the Files tab and are clickable", async ({
   await testFilterPresence(page, ANVIL_TABS.FILES, ANVIL_FILTER_NAMES);
 });
 
-test("Check that the first filter on the Datasets tab creates at least one checkbox, and that checking up to the first five does not cause an error and does not cause there to be no entries in the table", async ({
+test("Check that an arbitrary filter on the Datasets tab creates at least one checkbox, and that checking up to the first five does not cause an error and does not cause there to be no entries in the table", async ({
   page,
 }) => {
   // Goto the datasets tab
@@ -77,13 +77,7 @@ test("Check that the first filter on the Datasets tab creates at least one check
   // Select a filter
   await page
     .getByRole("button")
-    .getByText(
-      filterRegex(
-        ANVIL_FILTER_NAMES[
-          Math.floor(Math.random() * ANVIL_FILTER_NAMES.length)
-        ]
-      )
-    )
+    .getByText(filterRegex(ANVIL_FILTER_NAMES[FILTER_INDEX_LIST[0]]))
     .click();
   // Expect all checkboxes to be unchecked initially and to work properly
   await expect(page.getByRole("checkbox").first()).toBeVisible();

e2e/anvil/anvil-tabs.ts

@@ -94,7 +94,7 @@ export const ANVIL_TABS: AnvilCMGTabCollection = {
       exportActionButtonText: "Open Terra",
       exportRequestButtonText: "Request Link",
       exportTabName: "Export",
-      exportUrlRegExp: /\.*\/export-to-terra/,
+      exportUrlRegExp: /\/export-to-terra/,
       newTabMessage:
         "If you are a new user or returning user, click sign in to continue.",
       requestLandingMessage:

e2e/testFunctions.ts

@@ -11,6 +11,9 @@ import {
 const TIMEOUT_EXPORT_REQUEST = 60000;
 const TIMEOUT_DOWNLOAD = 10000;
 
+// Filter length const for regexes
+const MAX_FILTER_LENGTH = 256;
+
 /**
  * Get an array of all visible column header names
  * @param page - a Playwright page object
@@ -365,7 +368,7 @@ export async function testPreSelectedColumns(
  * @returns a regular expression matching "[filterName] ([n])"
  */
 export const filterRegex = (filterName: string): RegExp =>
-  new RegExp(escapeRegExp(filterName) + "\\s+\\([0-9]+\\)\\s*");
+  new RegExp(escapeRegExp(filterName) + "\\s+\\(\\d+\\)\\s*");
 
 /**
  * Checks that each filter specified in filterNames is visible and can be
@@ -467,7 +470,7 @@ const getFirstNonEmptyFilterOptionInfo = async (
   let i = 0;
   while (filterToSelect === "" && i < MAX_FILTER_OPTIONS_TO_CHECK) {
     // Filter options display as "[text]\n[number]" , sometimes with extra whitespace, so we want the string before the newline
-    const filterOptionRegex = /^(.*)\n+([0-9]+)\s*$/;
+    const filterOptionRegex = /^(.*)\n+(\d+)\s*$/;
     filterOptionLocator = getNthFilterOptionLocator(page, i);
     const filterNameMatch = (await filterOptionLocator.innerText())
       .trim()
@@ -1004,7 +1007,7 @@ const hoverAndGetText = async (
   if (
     !columnDescription !== undefined &&
     columnDescription?.pluralizedLabel !== undefined &&
-    RegExp("\\s*[0-9]+ " + columnDescription.pluralizedLabel + "\\s*").test(
+    RegExp("\\s*\\d+ " + columnDescription.pluralizedLabel + "\\s*").test(
       cellText
     )
   ) {
@@ -1186,7 +1189,7 @@ export async function testIndexExportSummary(
   await expect(indexExportButtonLocator).toBeVisible();
   for (const detail of tab.indexExportPage.detailsToCheck) {
     // This Regexp gets a decimal number, some whitespace, then the name of the detail, matching how the detail box appears to Playwright.
-    const detailBoxRegexp = RegExp(`^([0-9]+\\.[0-9]+k)\\s*${detail}$`);
+    const detailBoxRegexp = RegExp(`^(\\d+\\.\\d+k)\\s*${detail}$`);
     // This gets the detail's value. The .trim() is necessary since innertext adds extraneous whitespace on Webkit
     const headerValueArray = (await page.getByText(detailBoxRegexp).innerText())
       .trim()
@@ -1217,10 +1220,9 @@ export async function testIndexExportSummary(
   return true;
 }
 
-const PAGE_COUNT_REGEX = /Page [0-9]+ of [0-9]+/;
+const PAGE_COUNT_REGEX = /Page \d+ of \d+/;
 const BACK_BUTTON_TEST_ID = "WestRoundedIcon";
 const FORWARD_BUTTON_TEST_ID = "EastRoundedIcon";
-const ERROR = "ERROR";
 const MAX_PAGINATIONS = 200;
 
 /**
@@ -1236,7 +1238,7 @@ export async function testFirstPagePagination(
   await expect(getFirstRowNthColumnCellLocator(page, 0)).toBeVisible();
   // Should start on first page
   await expect(page.getByText(PAGE_COUNT_REGEX, { exact: true })).toHaveText(
-    /Page 1 of [0-9]+/
+    /Page 1 of \d+/
   );
   // Forward button should start enabled
   await expect(
@@ -1270,42 +1272,43 @@ export async function filterAndTestLastPagePagination(
   await expect(page.getByRole("checkbox").first()).toBeVisible();
   const filterTexts = await page
     .getByRole("button")
-    .filter({ hasText: /([0-9]+)[\n\s]*$/ })
+    .filter({ hasText: RegExp("(\\d{1," + MAX_FILTER_LENGTH + "})[\\s]*$") })
     .allInnerTexts();
   // Get the filter with the lowest associated count
-  const filterCounts = filterTexts
-    .map((filterText) =>
-      (
-        (filterText.match(/[^a-zA-Z0-9]+([0-9]+)[\n\s]*$/) ?? [
-          undefined,
-          "",
-        ])[1] ?? ERROR
-      ).trim()
+  const validFilterCounts = filterTexts
+    .map(
+      // Get filter counts
+      (filterOption) =>
+        filterOption
+          .split("\n")
+          .reverse()
+          .map((x) => Number(x))
+          .find((x) => !isNaN(x) && x !== 0) ?? -1
     )
-    .map((numberText) => parseInt(numberText))
     .filter(
+      /// Filter for counts that will produce a useful number of paginations
       (n) =>
         !isNaN(n) &&
         n > (tab.maxPages ?? 0) * 3 &&
         n < (tab.maxPages ?? 0) * MAX_PAGINATIONS
     );
-  if (filterCounts.length == 0) {
+  if (validFilterCounts.length == 0) {
     console.log(
-      "PAGINATION LAST PAGE: Test would involve too many paginations, so halting"
+      "PAGINATION LAST PAGE: Test would involve too many or too few paginations, so halting"
     );
     return false;
   }
-  const minFilterValue = Math.min(...filterCounts);
+  const minFilterValue = Math.min(...validFilterCounts);
   await page
     .getByRole("button")
-    .filter({ hasText: RegExp(`${minFilterValue}[\\n\\s]*$`) })
+    .filter({ hasText: RegExp(`${minFilterValue}[\\s]*$`) })
     .click();
   await page.locator("body").click();
   await expect(getFirstRowNthColumnCellLocator(page, 0)).toBeVisible();
 
   // Should start on first page, and there should be multiple pages available
   await expect(page.getByText(PAGE_COUNT_REGEX, { exact: true })).toHaveText(
-    /Page 1 of [0-9]+/
+    /Page 1 of \d+/
   );
   await expect(
     page.getByText(PAGE_COUNT_REGEX, { exact: true })
@@ -1368,7 +1371,7 @@ export async function testPaginationContent(
 
   // Should start on first page
   await expect(page.getByText(PAGE_COUNT_REGEX, { exact: true })).toHaveText(
-    /Page 1 of [0-9]+/
+    /Page 1 of \d+/
   );
   const maxPages = 5;
   const FirstTableEntries = [];
@@ -1384,7 +1387,7 @@ export async function testPaginationContent(
       .click();
     // Expect the page count to have incremented
     await expect(page.getByText(PAGE_COUNT_REGEX, { exact: true })).toHaveText(
-      RegExp(`Page ${i} of [0-9]+`)
+      RegExp(`Page ${i} of \\d+`)
     );
     // Expect the back button to be enabled
     await expect(
@@ -1417,7 +1420,7 @@ export async function testPaginationContent(
       .click();
     // Expect page number to be correct
     await expect(page.getByText(PAGE_COUNT_REGEX, { exact: true })).toHaveText(
-      RegExp(`Page ${maxPages - i - 1} of [0-9]+`)
+      RegExp(`Page ${maxPages - i - 1} of \\d+`)
     );
     // Expect page entry to be consistent with forward pagination
     await expect(firstElementTextLocator).toHaveText(OldFirstTableEntry);