Pulling fix/genome-page-linting into develop

apps/dicty-frontpage/src/common/data/mockContent.ts

@@ -1,4 +1,3 @@
-/* eslint-disable camelcase */
 const CONTENT_STRING = `{"root":{"children":[{"children":[{"detail":0,"format":0,"mode":"normal","style":"","text":"Annual International Dictyostelium Conference","type":"text","version":1}],"direction":"ltr","format":"","indent":0,"type":"heading","version":1,"tag":"h1"},{"children":[{"children":[{"detail":0,"format":0,"mode":"normal","style":"","text":"International conferences dedicated to ","type":"text","version":1},{"detail":0,"format":2,"mode":"normal","style":"","text":"Dictyostelium","type":"text","version":1},{"detail":0,"format":0,"mode":"normal","style":"","text":" started in  1977 with the meeting in Sardinia, and continued on a roughly 3-year  cycle into the 1980's. However, as the field became more active, more  local meetings sprang up to fill the gaps in the cycle. Notable amongst  these was an annual series in the UK, which gradually became more  international. By the late 1980's with the successive meetings at  Amsterdam, Oxford, Airlie and Cambridge, the current pattern of annual  meetings was established. Interestingly in the late 1990's as the field  expanded further, local meetings were re-started in several countries.     ","type":"text","version":1}],"direction":"ltr","format":"","indent":0,"type":"paragraph","version":1}],"direction":"ltr","format":"","indent":0,"type":"flex-layout","version":1}],"direction":"ltr","format":"","indent":0,"type":"root","version":1}}`
 const mockContent = [
   {

apps/dicty-frontpage/src/common/data/superuser.ts

@@ -1,4 +1,3 @@
-/* eslint-disable camelcase */
 export const testPermission = {
   id: "1",
   level: "test",

apps/dicty-frontpage/src/common/utils/citation.ts

@@ -1,26 +1,17 @@
 import { pipe } from "fp-ts/function"
-import { getOrElse as OgetOrElse } from "fp-ts/Option"
 import {
   map as Amap,
   last,
   compact as Acompact,
   intersperse as Aintersperse,
-  foldLeft as AfoldLeft,
-  foldMap as AfoldMap,
   reduce as Areduce,
-  splitAt as AsplitAt,
-  updateAt as AupdateAt,
-  zero as Azero,
 } from "fp-ts/Array"
 import {
   type NonEmptyArray,
-  splitAt as NEAsplitAt,
   last as NEAlast,
   init as NEAinit,
-  intersperse as NEAintersperse,
 } from "fp-ts/NonEmptyArray"
 import { bindTo as IbindTo, let as Ilet } from "fp-ts/Identity"
-import { Do as ODo, bind as Obind, let as Olet } from "fp-ts/Option"
 import { slice, trimRight } from "fp-ts/string"
 import { match } from "ts-pattern"
 import { type PublicationItem } from "../hooks/useFetchPublications"

apps/dicty-frontpage/src/database/index.ts

@@ -1,4 +1,3 @@
-/* eslint-disable camelcase */
 import { BrowserLevel } from "browser-level"
 import { mockContent } from "../common/data/mockContent"
 import { mockSuperuser } from "../common/data/superuser"

apps/genome-page/additional.d.ts

@@ -1,7 +1,9 @@
 /// <reference types="next" />
 import "typescript"
+
 declare global {
   namespace NodeJS {
+    // eslint-disable-next-line unicorn/prevent-abbreviations
     interface ProcessEnv {
       NEXT_PUBLIC_BASENAME: string
       NEXT_PUBLIC_GA_TRACKING_ID: string

apps/genome-page/common/@types/dicty-components-login.d.ts

@@ -1 +1,2 @@
+/* eslint-disable unicorn/filename-case */
 declare module "dicty-components-login"

apps/genome-page/common/@types/dicty-components-navbar.d.ts

@@ -1 +1,2 @@
+/* eslint-disable unicorn/filename-case */
 declare module "dicty-components-navbar"

apps/genome-page/common/hooks/WikiDisplay.tsx

@@ -1,40 +1,44 @@
 // group of functions that maps the markdown content/error to the corresponding react component
-import * as E from "fp-ts/Either"
-import * as F from "fp-ts-std/Function"
-import WikiContainer from "../../components/features/CommunityAnnotations/WikiContainer"
-import WikiLoader from "../../components/features/CommunityAnnotations/WikiLoader"
-
-interface WikiContentProps {
+import {
+  type Either,
+  isRight as EisRight,
+  isLeft as EisLeft,
+} from "fp-ts/Either"
+import { guard } from "fp-ts-std/Function"
+import { WikiContainer } from "../../components/features/CommunityAnnotations/WikiContainer"
+import { WikiLoader } from "../../components/features/CommunityAnnotations/WikiLoader"
+
+interface WikiContentProperties {
   markdown?: string
   loading: boolean
 }
 
 // type for Either monad
-export type WikiContentEither = E.Either<string, WikiContentProps>
+export type WikiContentEither = Either<string, WikiContentProperties>
 
 // predicate function that checks is the fetching is under process
-const isLoading = (ma: WikiContentEither) => E.isRight(ma) && ma.right.loading
+const isLoading = (ma: WikiContentEither) => EisRight(ma) && ma.right.loading
 
 // predicate function to indicate if the fetching is completed
 const isNotLoading = (ma: WikiContentEither) =>
-  E.isRight(ma) && !ma.right.loading
+  EisRight(ma) && !ma.right.loading
 
 // react component for loading state
 const loaderDisplay = () => <WikiLoader />
 
 // react component for error display
-const errDisplay = (ma: WikiContentEither) => E.isLeft(ma) && <WikiContainer />
+const errorDisplay = (ma: WikiContentEither) => EisLeft(ma) && <WikiContainer />
 
 // react component for display markdown content
 const nameDisplay = (ma: WikiContentEither) =>
-  E.isRight(ma) && <WikiContainer markdown={ma.right.markdown as string} />
+  EisRight(ma) && <WikiContainer markdown={ma.right.markdown as string} />
 
 // react component when something unexpected happened
 const defaultDisplay = () => <h2>Not sure what happened</h2>
 
 // this function maps three conditions, error,success or loading to a react component
-export const toOutput = F.guard([
+export const toOutput = guard([
   [isLoading, loaderDisplay],
-  [E.isLeft, errDisplay],
+  [EisLeft, errorDisplay],
   [isNotLoading, nameDisplay],
 ])(defaultDisplay)

apps/genome-page/common/hooks/useCreateApolloClient.test.tsx

@@ -1,3 +1,4 @@
+/* eslint-disable sonarjs/no-duplicate-string */
 import { isMutation, getGraphQLServer } from "./useCreateApolloClient"
 
 describe("isMutation function", () => {

apps/genome-page/common/hooks/useCreateApolloClient.tsx

@@ -13,17 +13,16 @@ import version from "dicty-graphql-schema/package.json"
 const SCHEMA_VERSION_KEY = "gene-apollo-schema-version"
 const GENE_CACHE_KEY = "gene-apollo-cache-persist"
 
-const mutationList = ["Logout"]
+const mutationList = new Set(["Logout"])
 
-const isMutation = (value: string) => {
-  if (mutationList.includes(value)) {
-    return true
-  }
-  return false
-}
+const isMutation = (value: string) => mutationList.has(value)
 
-const getGraphQLServer = (url: string, deployEnv: string, origin: string) => {
-  if (deployEnv === "staging" && origin === "https://dictycr.org") {
+const getGraphQLServer = (
+  url: string,
+  deployEnvironment: string,
+  origin: string,
+) => {
+  if (deployEnvironment === "staging" && origin === "https://dictycr.org") {
     return process.env.NEXT_PUBLIC_ALT_GRAPHQL_SERVER
   }
   return url
@@ -42,6 +41,7 @@ const authLink = setContext((request, { headers }) => {
 })
 
 const createApolloLink = (server: string): ApolloLink =>
+  // eslint-disable-next-line unicorn/prefer-spread -- this .concat is not Array.concat
   authLink.concat(
     createHttpLink({
       uri: `${server}/graphql`,
@@ -94,4 +94,4 @@ const useCreateApolloClient = () => {
 }
 
 export { isMutation, getGraphQLServer }
-export default useCreateApolloClient
+export { useCreateApolloClient }

apps/genome-page/common/hooks/useGithubWiki.ts

@@ -1,71 +1,73 @@
 // group of functions that receives an git url and provides a promise to resolve it to its
 // markdown component
 import { pipe, flow } from "fp-ts/lib/function"
-import * as E from "fp-ts/lib/Either"
-import * as TE from "fp-ts/lib/TaskEither"
+import { toError } from "fp-ts/lib/Either"
+import { of, tryCatch, chain, map, mapLeft } from "fp-ts/lib/TaskEither"
 import { clone } from "isomorphic-git"
-import * as S from "fp-ts/string"
+import { Semigroup } from "fp-ts/string"
 import { intercalate } from "fp-ts/Semigroup"
 import http from "isomorphic-git/http/web"
 import FS from "@isomorphic-git/lightning-fs"
 
-export interface DirFileProps {
+export interface DirectoryFileProperties {
   dir: string
   file: string
   url: string
   browserFS: FS
 }
 
 // The main wrapper function or hook
-export function cloneGithubWiki(props: DirFileProps) {
-  const defaultCloneParams = {
-    http: http,
-    fs: props.browserFS,
+export function cloneGithubWiki(properties: DirectoryFileProperties) {
+  const defaultCloneParameters = {
+    http,
+    fs: properties.browserFS,
     corsProxy: "https://cors.isomorphic-git.org",
   }
-  const defaultSep = "/"
+  const defaultSeparator = "/"
 
   // function that converts the data to a monad that handle promise
-  const wrapper = (props: DirFileProps) => TE.of(props)
+  const wrapper = (properties_: DirectoryFileProperties) => of(properties_)
 
   // function that runs the clone api and returns a promise, handles both the
   // success and error conditons.
-  const executeCloneRepo = ({ dir, url, file }: DirFileProps) =>
-    TE.tryCatch(async () => {
-      await clone({ dir, url, ...defaultCloneParams })
-      return { dir, url, file } as DirFileProps
-    }, E.toError)
+  const executeCloneRepo = ({ dir, url, file }: DirectoryFileProperties) =>
+    tryCatch(async () => {
+      await clone({ dir, url, ...defaultCloneParameters })
+      return { dir, url, file } as DirectoryFileProperties
+    }, toError)
   // const errLogger = TE.fromIOK(Console.error)
   // const infoLogger = TE.fromIOK(Console.info)
 
-  // function that extract the error message from the Error object
-  const errMsgExtract = (err: Error) => err.message
-
   // function that constructs the markdown file path inside the git repo
-  const addPath = ({ dir, file }: DirFileProps) => {
-    const pathDelimGroup = pipe(S.Semigroup, intercalate(defaultSep))
+  const addPath = ({ dir, file }: DirectoryFileProperties) => {
+    const pathDelimGroup = pipe(Semigroup, intercalate(defaultSeparator))
+    // eslint-disable-next-line unicorn/prefer-spread -- this .concat is not Array.concat
     return pathDelimGroup.concat(dir, file)
   }
 
   // function that read the markdown file from the git repo. Also handles the error.
   const readFileFromRepo = (path: string) =>
-    TE.tryCatch(async () => {
-      const buffer = await props.browserFS.promises.readFile(path, {
+    tryCatch(async () => {
+      const buffer = await properties.browserFS.promises.readFile(path, {
         encoding: "utf8",
       })
       return buffer.toString()
-    }, E.toError)
+    }, toError)
+
+  // function that extract the error message from the Error object
+  // eslint-disable-next-line unicorn/consistent-function-scoping -- It's nice to keep this function here because these functions are defined in the order they are used in the flow below.
+  const errorMessageExtract = (error: Error) => error.message
 
   // construct a pipeline from all the functions
   const payload = flow(
     wrapper,
-    TE.chain(executeCloneRepo),
+    chain(executeCloneRepo),
     // TE.chainFirstIOK(infoLogger),
-    TE.map(addPath),
+    map(addPath),
     // TE.chainFirstIOK(infoLogger),
-    TE.chain(readFileFromRepo),
+    chain(readFileFromRepo),
     // TE.chainFirstIOK(infoLogger),
-    TE.mapLeft(errMsgExtract),
+    mapLeft(errorMessageExtract),
   )
-  return payload(props)
+  return payload(properties)
 }

apps/genome-page/common/hooks/useGoogleAnalytics.tsx

@@ -10,13 +10,13 @@ const useGoogleAnalytics = () => {
     const setGoogleAnalytics = async () => {
       try {
         const module = await import("react-ga")
-        const trackingID = process.env.NEXT_PUBLIC_GA_TRACKING_ID
+        const trackingID = process.env.NEXT_PUBLIC_GA_TRACKING_ID as string
         const basename = process.env.NEXT_PUBLIC_BASENAME
         const page = basename + router.pathname
-        let ReactGA = module.default
+        const ReactGA = module.default
 
         ReactGA.initialize(trackingID)
-        ReactGA.set({ page: page, anonymizeIp: true })
+        ReactGA.set({ page, anonymizeIp: true })
         ReactGA.pageview(page)
 
         // also make sure to detect pageviews from bfcache
@@ -26,8 +26,9 @@ const useGoogleAnalytics = () => {
             ReactGA.pageview(page)
           }
         })
-      } catch (e) {
-        console.error("could not load react-ga module", JSON.stringify(e))
+      } catch (error) {
+        // eslint-disable-next-line no-console
+        console.error("could not load react-ga module", JSON.stringify(error))
       }
     }
 
@@ -37,4 +38,4 @@ const useGoogleAnalytics = () => {
   }, [router.pathname])
 }
 
-export default useGoogleAnalytics
+export { useGoogleAnalytics }