chore: updated dev dependencies (#4309) (#4318)

* chore: updated typescript (#4309)

* chore: updated eslint plugins (#4309)

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

* chore: updated and ran prettier (#3409)

* chore: updated commitlint (#3409)

* chore: updated babel-loader (#4309)

* chore: updated got (#4309)

* chore: updated playwright (#4309)

* chore: updated husky (#4309)

* chore: updated jest (#4309)

* fix: moved next-mdx-remote to prod dependencies (#4309)

* fix: renamed Error to MyError (#4309)

* chore: diabled no-nested-conditional eslint rule (#4309)

Author: Jonah Paten

.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": "off"
   },
   "overrides": [
     {

.husky/commit-msg

@@ -1,6 +1,3 @@
-#!/usr/bin/env sh
-. "$(dirname -- "$0")/_/husky.sh"
-
 echo "Checking commit message"
 
 # Check for issue number

.husky/pre-commit

@@ -1,6 +1,3 @@
-#!/bin/sh
-. "$(dirname "$0")/_/husky.sh"
-
 echo '🏗️👷 Checking your project before committing'
 
 # Check Prettier

.prettierignore

@@ -17,3 +17,6 @@ build
 
 # dependencies
 node_modules
+
+# other (avoids breaking a link)
+app/components/common/MDXContent/hca-dcp/downloadBatchCorrectionWarning.mdx

.prettierrc.json

@@ -1 +1,3 @@
-{}
+{
+  "trailingComma": "es5"
+}

__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/apis/azul/common/utils.ts

@@ -70,7 +70,7 @@ export function isNullOrUndefined(value: any): boolean {
  */
 export function processAggregatedOrArrayValue<
   T,
-  K extends KeyOfTypeStringOrNullArray<T>
+  K extends KeyOfTypeStringOrNullArray<T>,
 >(responseValues: T[], key: K): string[] {
   // Aggregate key values across response values.
   const values = aggregateResponseValues(
@@ -91,7 +91,7 @@ export function processAggregatedOrArrayValue<
  */
 export function processAggregatedBooleanOrArrayValue<
   T,
-  K extends KeyOfTypeBooleanOrNullArray<T>
+  K extends KeyOfTypeBooleanOrNullArray<T>,
 >(responseValues: T[], key: K): string[] {
   // Aggregate key values across response values.
   const values = aggregateResponseValues(
@@ -114,7 +114,7 @@ export function processAggregatedBooleanOrArrayValue<
  */
 export function processAggregatedNumberEntityValue<
   T,
-  K extends KeyOfTypeNumberOrNull<T>
+  K extends KeyOfTypeNumberOrNull<T>,
 >(responseValues: T[], key: K): number {
   // Aggregate key values across response values.
   return aggregateNumericalResponseValues(responseValues, key);
@@ -129,7 +129,7 @@ export function processAggregatedNumberEntityValue<
  */
 export function processEntityArrayValue<
   T,
-  K extends KeyOfTypeStringOrNullArray<T>
+  K extends KeyOfTypeStringOrNullArray<T>,
 >(responseValues: T[], key: K, label = LABEL.UNSPECIFIED): string[] {
   // Response values should be a singleton array; check for at least one value here.
   if (responseValues.length === 0) {
@@ -202,7 +202,7 @@ export function processNumberEntityValue<T, K extends KeyOfTypeNumberOrNull<T>>(
  */
 function aggregateNumericalResponseValues<
   T,
-  K extends KeyOfTypeNumberOrNull<T>
+  K extends KeyOfTypeNumberOrNull<T>,
 >(responseValues: T[], key: K): number {
   return responseValues
     .map((responseValue) => responseValue[key] as unknown as number)
@@ -217,7 +217,7 @@ function aggregateNumericalResponseValues<
  */
 function aggregateResponseValues<
   T,
-  K extends KeyOfTypeStringOrNullArray<T> | KeyOfTypeBooleanOrNullArray<T>
+  K extends KeyOfTypeStringOrNullArray<T> | KeyOfTypeBooleanOrNullArray<T>,
 >(responseValues: T[], key: K): StringOrNullArray | BooleanOrNullArray {
   return responseValues
     .filter((responseValue) => !!responseValue[key])

app/apis/azul/hca-dcp/archivePreview/archivePreview.ts

@@ -52,7 +52,7 @@ export async function fetchProjectMatrixArchiveFiles(
     const response = await fetch(url);
     const result = await response.json();
     return bindArchiveFiles(result);
-  } catch (error) {
+  } catch {
     return [];
   }
 }

app/apis/catalog/anvil-catalog/common/utils.ts

@@ -61,7 +61,7 @@ export const getConsortiumTitle = (
 };
 
 export const anvilCatalogStudyInputMapper = <
-  StudyType extends AnVILCatalogStudyAny
+  StudyType extends AnVILCatalogStudyAny,
 >(
   input: StudyType
 ): StudyType => {

app/components/Detail/components/GeneratedMatricesTables/components/ArchivePreviewDialog/components/ArchivePreviewTable/archivePreviewTable.tsx

@@ -25,7 +25,7 @@ export interface ArchivePreviewTableProps {
  */
 function getArchivePreviewTableColumns<
   T extends RowData,
-  TData = unknown
+  TData = unknown,
 >(): ColumnDef<T, TData>[] {
   return [
     {

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/utils/tsvParser.ts

@@ -53,7 +53,7 @@ export const readDir = async function readDir(
   try {
     return fs.readdirSync(dir, options);
     // eslint-disable-next-line no-empty -- copied from readFile function
-  } catch (err) {}
+  } catch {}
 };
 
 /**
@@ -72,7 +72,7 @@ export const readFile = async function readFile(
     const jsonDirectory = process.cwd();
     return fs.readFileSync(jsonDirectory + "/" + file, options);
     // eslint-disable-next-line no-empty -- copied from anvil-portal
-  } catch (err) {}
+  } catch {}
 };
 
 /**

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/projectMapper/projectMapper.ts

@@ -296,7 +296,7 @@ function isContributorDataCurator(
 function isValidUrl(testUrl: string): boolean {
   try {
     return Boolean(new URL(testUrl));
-  } catch (e) {
+  } catch {
     return false;
   }
 }

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 */
     }),
   };
 };
@@ -1642,7 +1648,9 @@ function getAnalysisPortalKeyValueFn(
     const [, value] = keyValue;
     if (value && typeof value === "string") {
       const url = analysisPortals.find(({ label }) => label === value)?.url;
-      url && window.open(url, ANCHOR_TARGET.BLANK);
+      if (url) {
+        window.open(url, ANCHOR_TARGET.BLANK);
+      }
     }
   };
 }
@@ -1957,7 +1965,7 @@ export function getGeneratedMatricesActionsColumnDef<T>(): ColumnDef<T> {
  * @returns anatomical entity column def.
  */
 export function getGeneratedMatricesAnatomicalEntityColumnDef<
-  T
+  T,
 >(): ColumnDef<T> {
   return {
     accessorKey: HCA_DCP_CATEGORY_KEY.ORGAN,
@@ -1978,7 +1986,7 @@ export function getGeneratedMatricesAnatomicalEntityColumnDef<
  * @returns content description column def.
  */
 export function getGeneratedMatricesContentDescriptionColumnDef<
-  T
+  T,
 >(): ColumnDef<T> {
   return {
     accessorKey: HCA_DCP_CATEGORY_KEY.CONTENT_DESCRIPTION,
@@ -2051,7 +2059,7 @@ export function getGeneratedMatricesGenusSpeciesColumnDef<T>(): ColumnDef<T> {
  * @returns library construction method column def.
  */
 export function getGeneratedMatricesLibraryConstructionMethodColumnDef<
-  T
+  T,
 >(): ColumnDef<T> {
   return {
     accessorKey: HCA_DCP_CATEGORY_KEY.LIBRARY_CONSTRUCTION_METHOD,
@@ -2072,7 +2080,7 @@ export function getGeneratedMatricesLibraryConstructionMethodColumnDef<
  * @returns matrix cell count column def.
  */
 export function getGeneratedMatricesMatrixCellCountColumnDef<
-  T
+  T,
 >(): ColumnDef<T> {
   return {
     accessorKey: HCA_DCP_CATEGORY_KEY.MATRIX_CELL_COUNT,
@@ -2416,12 +2424,15 @@ export const renderWhenUnAuthenticated = (
  * @returns total cells from cellSuspensions.
  */
 function rollUpTotalCells(entityResponse: EntityResponse): number | null {
-  return entityResponse.cellSuspensions.reduce((acc, { totalCells }) => {
-    if (totalCells) {
-      acc = (acc ?? 0) + totalCells;
-    }
-    return acc;
-  }, null as null | number);
+  return entityResponse.cellSuspensions.reduce(
+    (acc, { totalCells }) => {
+      if (totalCells) {
+        acc = (acc ?? 0) + totalCells;
+      }
+      return acc;
+    },
+    null as null | number
+  );
 }
 
 /**

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: