chore: update dev dependencies (#3427) (#3428)

* chore: update typescript (#3427)

* chore: update typescript-eslint (#3427)

* chore: update eslint plugins (#3427)

* feat: configure/resolve sonarjs errors (#3427)

* chore: update prettier (#3427)

* style: configure prettier and fix remaining errors (#3427)

* chore: update commitlint (#3427)

* chore: update jest (#3427)

* chore: update husky (#3427)

* chore: update csv-parse and got (#3427)

* fix: update hook for latest version of husky (#3427)

* chore: move dependencies used in app out of dev dependencies (#3427)

* chore: move slugify out of dev dependencies (#3427)

* content: remove link that now points to incorrect site (#3427)

Author: hunterckx

.eslintrc.json

@@ -15,7 +15,7 @@
     "prettier",
     "plugin:prettier/recommended",
     "next",
-    "plugin:sonarjs/recommended",
+    "plugin:sonarjs/recommended-legacy",
     "plugin:eslint-comments/recommended"
   ],
   "rules": {
@@ -58,7 +58,8 @@
     "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"
   },
   "overrides": [
     {

.husky/commit-msg

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

.prettierrc.json

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

components/Consortia/CSER/components/Publications/publications.tsx

@@ -5,13 +5,16 @@ import publications from "./publications.json";
 import { Publications as PublicationsByYear } from "./publications.styles";
 
 export const Publications = (): JSX.Element => {
-  const publicationsByYear = publications.reduce((byYear, publication) => {
-    (
-      byYear[publication.publicationYear] ||
-      (byYear[publication.publicationYear] = [])
-    ).push(publication);
-    return byYear;
-  }, {} as Record<string, typeof publications>);
+  const publicationsByYear = publications.reduce(
+    (byYear, publication) => {
+      (
+        byYear[publication.publicationYear] ||
+        (byYear[publication.publicationYear] = [])
+      ).push(publication);
+      return byYear;
+    },
+    {} as Record<string, typeof publications>
+  );
 
   const { compare } = new Intl.Collator("en");
 

components/Consortia/CSER/components/Resources/resources.tsx

@@ -86,10 +86,10 @@ export const Resources = (): JSX.Element => {
             A database of genes that, when somatically altered in cancer, are
             directly linked to a clinical action. Created by CanSeq:
           </p>
-          <p>http://www.broadinstitute.org/cancer/cga/target</p>
+          <p>https://www.broadinstitute.org/cancer/cga/target</p>
           {/* <Link */}
-          {/*   label="http://www.broadinstitute.org/cancer/cga/target" */}
-          {/*   url="http://www.broadinstitute.org/cancer/cga/target" */}
+          {/*   label="https://www.broadinstitute.org/cancer/cga/target" */}
+          {/*   url="https://www.broadinstitute.org/cancer/cga/target" */}
           {/* /> */}
         </div>
         <div>
@@ -101,10 +101,10 @@ export const Resources = (): JSX.Element => {
             A heuristic algorithm for clinical interpretation of cancer genome
             sequencing data. Created by CanSeq:
           </p>
-          <p>http://www.broadinstitute.org/cancer/cga/phial</p>
+          <p>https://www.broadinstitute.org/cancer/cga/phial</p>
           {/* <Link */}
-          {/*   label="http://www.broadinstitute.org/cancer/cga/phial" */}
-          {/*   url="http://www.broadinstitute.org/cancer/cga/phial" */}
+          {/*   label="https://www.broadinstitute.org/cancer/cga/phial" */}
+          {/*   url="https://www.broadinstitute.org/cancer/cga/phial" */}
           {/* /> */}
         </div>
         <div>
@@ -137,7 +137,7 @@ export const Resources = (): JSX.Element => {
             Proband is an app for taking family history pedigrees, designed
             exclusively for the iPad. Created by PediSeq.
           </p>
-          {/* <Link label="http://probandapp.com" url="http://probandapp.com" /> */}
+          {/* <Link label="https://probandapp.com" url="https://probandapp.com" /> */}
         </div>
         <div>
           <TextBodyLarge500>
@@ -148,7 +148,7 @@ export const Resources = (): JSX.Element => {
             to allow adults undergoing genomic testing to record their
             preferences about getting incidental or secondary results.
           </p>
-          <Link label="http://www.pigsr.org" url="http://www.pigsr.org" />
+          <Link label="https://www.pigsr.org" url="https://www.pigsr.org" />
         </div>
         <div>
           <TextBodyLarge500>
@@ -159,10 +159,10 @@ export const Resources = (): JSX.Element => {
             A NEJM interactive graphic on clinical genome and exome sequencing.
             Created by ClinSeq and MedSeq:
           </p>
-          <p>http://www.nejm.org</p>
+          <p>https://www.nejm.org</p>
           {/* <Link */}
-          {/*   label="http://www.nejm.org" */}
-          {/*   url="http://www.nejm.org/action/showMediaPlayer?doi=10.1056/NEJMra1312543&aid=NEJMra1312543_attach_1" */}
+          {/*   label="https://www.nejm.org" */}
+          {/*   url="https://www.nejm.org/action/showMediaPlayer?doi=10.1056/NEJMra1312543&aid=NEJMra1312543_attach_1" */}
           {/* /> */}
         </div>
       </Accordion>
@@ -207,8 +207,8 @@ export const Resources = (): JSX.Element => {
           <TextBodyLarge500>Medscape</TextBodyLarge500>
           <p>Medscape offers diverse topics in its online CME library:</p>
           <Link
-            label="http://www.medscape.org/resource/genomic-medicine/cme"
-            url="http://www.medscape.org/resource/genomic-medicine/cme"
+            label="https://www.medscape.org/resource/genomic-medicine/cme"
+            url="https://www.medscape.org/resource/genomic-medicine/cme"
           />
         </div>
       </Accordion>
@@ -220,8 +220,8 @@ export const Resources = (): JSX.Element => {
             among human variations and phenotypes with supporting evidence:
           </p>
           <Link
-            label="http://www.ncbi.nlm.nih.gov/clinvar"
-            url="http://www.ncbi.nlm.nih.gov/clinvar"
+            label="https://www.ncbi.nlm.nih.gov/clinvar"
+            url="https://www.ncbi.nlm.nih.gov/clinvar"
           />
         </div>
         <div>
@@ -231,8 +231,8 @@ export const Resources = (): JSX.Element => {
             Exome Sequencing Project (ESP):
           </p>
           <Link
-            label="http://evs.gs.washington.edu/EVS"
-            url="http://evs.gs.washington.edu/EVS"
+            label="https://evs.gs.washington.edu/EVS"
+            url="https://evs.gs.washington.edu/EVS"
           />
         </div>
         <div>
@@ -245,8 +245,8 @@ export const Resources = (): JSX.Element => {
             investigated the interaction of genotype and phenotype:
           </p>
           <Link
-            label="http://www.ncbi.nlm.nih.gov/gap"
-            url="http://www.ncbi.nlm.nih.gov/gap"
+            label="https://www.ncbi.nlm.nih.gov/gap"
+            url="https://www.ncbi.nlm.nih.gov/gap"
           />
         </div>
         <div>
@@ -255,7 +255,7 @@ export const Resources = (): JSX.Element => {
             The UCSC Genome Browser, containing the reference sequence and
             working draft assemblies for a large collection of genomes:
           </p>
-          <Link label="http://genome.ucsc.edu" url="http://genome.ucsc.edu" />
+          <Link label="https://genome.ucsc.edu" url="https://genome.ucsc.edu" />
         </div>
         <div>
           <TextBodyLarge500>
@@ -266,8 +266,8 @@ export const Resources = (): JSX.Element => {
             authoritative compendium of human genes and genetic phenotypes:
           </p>
           <Link
-            label="http://www.ncbi.nlm.nih.gov/omim"
-            url="http://www.ncbi.nlm.nih.gov/omim"
+            label="https://www.ncbi.nlm.nih.gov/omim"
+            url="https://www.ncbi.nlm.nih.gov/omim"
           />
         </div>
         <div>
@@ -277,8 +277,8 @@ export const Resources = (): JSX.Element => {
             descriptions with a clinical focus:
           </p>
           <Link
-            label="http://www.genereviews.org"
-            url="http://www.genereviews.org"
+            label="https://www.genereviews.org"
+            url="https://www.genereviews.org"
           />
         </div>
         <div>
@@ -287,16 +287,16 @@ export const Resources = (): JSX.Element => {
             Genetics Home Reference, consumer-friendly information about the
             effects of genetic variations on human health:
           </p>
-          <Link label="http://ghr.nlm.nih.gov" url="http://ghr.nlm.nih.gov" />
+          <Link label="https://ghr.nlm.nih.gov" url="https://ghr.nlm.nih.gov" />
         </div>
         <div>
           <TextBodyLarge500>Center for Mendelian Genomics</TextBodyLarge500>
           <p>
             Center for Mendelian Genomics, will apply next-generation sequencing
             and computational approaches to discover the genes and variants that
-            underlie Mendelian conditions:
+            underlie Mendelian conditions.
           </p>
-          <Link label="http://mendelian.org/" url="http://mendelian.org" />
+          {/* <Link label="https://mendelian.org/" url="https://mendelian.org" /> */}
         </div>
         <div>
           <TextBodyLarge500>The CSER1 ELSI Literature Archive</TextBodyLarge500>

components/Home/components/Section/components/SectionHero/components/Carousel/components/Arrow/arrow.styles.ts

@@ -26,7 +26,9 @@ export const IconButton = styled(MIconButton, {
   & {
     background-color: ${white};
     border-radius: 50%;
-    box-shadow: inset 0 0 0 1px ${smokeDark}, 0 1px 0 0 ${black08};
+    box-shadow:
+      inset 0 0 0 1px ${smokeDark},
+      0 1px 0 0 ${black08};
     color: ${inkMain};
     position: absolute;
     top: 50%;

components/Home/components/Section/components/SectionHero/components/Carousel/components/Cards/cards.styles.ts

@@ -44,7 +44,9 @@ export const CardPositioner = styled("div")<Props>`
 
 export const Card = styled(MCard)`
   border: none;
-  box-shadow: ${elevation01}, inset 0 0 0 1px ${smokeMain};
+  box-shadow:
+    ${elevation01},
+    inset 0 0 0 1px ${smokeMain};
   display: flex;
   height: 100%;
   width: 100%;