Lint unicorn

eslint.config.mjs

@@ -25,6 +25,7 @@ export default [
       'plugin:@typescript-eslint/stylistic-type-checked',
       'plugin:react/recommended',
       'plugin:react-hooks/recommended',
+      'plugin:unicorn/recommended',
     ),
   ),
   {
@@ -50,6 +51,13 @@ export default [
     },
 
     rules: {
+      'unicorn/prevent-abbreviations': 'off',
+      'unicorn/no-null': 'off',
+      'unicorn/filename-case': 'off',
+      'unicorn/no-useless-undefined': 'off',
+      'unicorn/catch-error-name': 'off',
+      'unicorn/no-nested-ternary': 'off',
+      'unicorn/better-regex': 'off',
       '@typescript-eslint/no-unsafe-member-access': 'off',
       '@typescript-eslint/no-unsafe-argument': 'off',
       '@typescript-eslint/no-unsafe-assignment': 'off',
@@ -59,7 +67,12 @@ export default [
       '@typescript-eslint/ban-ts-comment': 'off',
       '@typescript-eslint/no-empty-function': 'off',
       '@typescript-eslint/require-await': 'off',
-
+      'no-console': [
+        'warn',
+        {
+          allow: ['error', 'warn'],
+        },
+      ],
       '@typescript-eslint/no-unused-vars': [
         'warn',
         {

package.json

@@ -60,6 +60,7 @@
     "eslint-plugin-prettier": "^5.1.0",
     "eslint-plugin-react": "^7.20.3",
     "eslint-plugin-react-hooks": "^4.6.0",
+    "eslint-plugin-unicorn": "^54.0.0",
     "mobx": "^6.10.2",
     "mobx-react": "^9.0.1",
     "mobx-state-tree": "^5.3.0",

src/LaunchMsaView/components/NewNCBIBlastQuery/NcbiBlastPanel.tsx

@@ -110,9 +110,9 @@ const NcbiBlastPanel = observer(function NcbiBlastPanel2({
         maxRows={10}
         fullWidth
         value={
-          !proteinSequence
-            ? 'Loading...'
-            : `>${getTranscriptDisplayName(selectedTranscript)}\n${proteinSequence}`
+          proteinSequence
+            ? `>${getTranscriptDisplayName(selectedTranscript)}\n${proteinSequence}`
+            : 'Loading...'
         }
         InputProps={{
           readOnly: true,

src/LaunchMsaView/components/NewNCBIBlastQuery/index.tsx

@@ -1,2 +1 @@
-import NcbiBlastPanel from './NcbiBlastPanel'
-export default NcbiBlastPanel
+export { default } from './NcbiBlastPanel'

src/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.tsx

@@ -23,6 +23,7 @@ import {
   getTranscriptDisplayName,
   getId,
   getTranscriptFeatures,
+  getGeneDisplayName,
 } from '../../util'
 import { fetchGeneList } from './fetchGeneList'
 import { preCalculatedLaunchView } from './preCalculatedLaunchView'
@@ -120,7 +121,7 @@ const PreLoadedMSA = observer(function PreLoadedMSA2({
                 await preCalculatedLaunchView({
                   userSelection,
                   session,
-                  newViewTitle: '',
+                  newViewTitle: getGeneDisplayName(ret),
                   view,
                   feature: ret,
                 })

src/MsaViewPanel/model.ts

@@ -1,7 +1,7 @@
 import { Instance, addDisposer, cast, types } from 'mobx-state-tree'
 import { autorun } from 'mobx'
 import { MSAModelF } from 'react-msaview'
-import { Feature, getSession, notEmpty } from '@jbrowse/core/util'
+import { Feature, getSession } from '@jbrowse/core/util'
 import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes'
 
@@ -101,7 +101,6 @@ export default function stateModelFactory() {
        * #getter
        */
       get transcriptToMsaMap() {
-        console.log(self.connectedFeature)
         return self.connectedFeature
           ? genomeToTranscriptSeqMapping(self.connectedFeature)
           : undefined
@@ -250,14 +249,14 @@ export default function stateModelFactory() {
           autorun(() => {
             const { mouseCol, mouseClickCol } = self
             const r1 =
-              mouseCol !== undefined
-                ? msaCoordToGenomeCoord({ model: self, coord: mouseCol })
-                : undefined
+              mouseCol === undefined
+                ? undefined
+                : msaCoordToGenomeCoord({ model: self, coord: mouseCol })
             const r2 =
-              mouseClickCol !== undefined
-                ? msaCoordToGenomeCoord({ model: self, coord: mouseClickCol })
-                : undefined
-            self.setConnectedHighlights([r1, r2].filter(notEmpty))
+              mouseClickCol === undefined
+                ? undefined
+                : msaCoordToGenomeCoord({ model: self, coord: mouseClickCol })
+            self.setConnectedHighlights([r1, r2].filter(f => !!f))
           }),
         )
 
@@ -268,9 +267,9 @@ export default function stateModelFactory() {
             const { connectedView, zoomToBaseLevel, mouseClickCol } = self
             const { assemblyManager } = getSession(self)
             const r2 =
-              mouseClickCol !== undefined
-                ? msaCoordToGenomeCoord({ model: self, coord: mouseClickCol })
-                : undefined
+              mouseClickCol === undefined
+                ? undefined
+                : msaCoordToGenomeCoord({ model: self, coord: mouseClickCol })
 
             if (!r2 || !connectedView) {
               return

src/utils/msa.ts

@@ -121,15 +121,21 @@ export async function launchMSA({
   onProgress: (arg: string) => void
 }) {
   onProgress(`Launching ${algorithm} MSA...`)
-  if (algorithm === 'clustalo') {
-    return runClustalOmega({ sequence, onProgress })
-  } else if (algorithm === 'muscle') {
-    return runMuscle({ sequence, onProgress })
-  } else if (algorithm === 'kalign') {
-    return runKalign({ sequence, onProgress })
-  } else if (algorithm === 'mafft') {
-    return runMafft({ sequence, onProgress })
-  } else {
-    throw new Error('unknown algorithm')
+  switch (algorithm) {
+    case 'clustalo': {
+      return runClustalOmega({ sequence, onProgress })
+    }
+    case 'muscle': {
+      return runMuscle({ sequence, onProgress })
+    }
+    case 'kalign': {
+      return runKalign({ sequence, onProgress })
+    }
+    case 'mafft': {
+      return runMafft({ sequence, onProgress })
+    }
+    default: {
+      throw new Error('unknown algorithm')
+    }
   }
 }

src/utils/ncbiBlast.ts

@@ -88,14 +88,14 @@ async function waitForRid({
     const res = await textfetch(
       `${BLAST_URL}?CMD=Get&FORMAT_OBJECT=SearchInfo&RID=${rid}`,
     )
-    if (res.match(/\s+Status=WAITING/m)) {
+    if (/\s+Status=WAITING/m.test(res)) {
       continue
-    } else if (res.match(/\s+Status=FAILED/m)) {
+    } else if (/\s+Status=FAILED/m.test(res)) {
       throw new Error(
         `BLAST ${rid} failed; please report to [email protected]`,
       )
-    } else if (res.match(/\s+Status=READY/m)) {
-      if (res.match(/\s+ThereAreHits=yes/m)) {
+    } else if (/\s+Status=READY/m.test(res)) {
+      if (/\s+ThereAreHits=yes/m.test(res)) {
         return true
       } else {
         throw new Error('No hits found')