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 [
     {