Lint

eslint.config.mjs

@@ -4,11 +4,10 @@ import eslintPluginReactHooks from 'eslint-plugin-react-hooks'
 import eslintPluginReactRefresh from 'eslint-plugin-react-refresh'
 import eslintPluginUnicorn from 'eslint-plugin-unicorn'
 import tseslint from 'typescript-eslint'
-import globals from 'globals'
 
 export default tseslint.config(
   {
-    ignores: ['**/dist/**/*'],
+    ignores: ['**/dist/**/*', 'esbuild.mjs', 'eslint.config.mjs', 'ucsc/*'],
   },
   {
     languageOptions: {
@@ -63,6 +62,11 @@ export default tseslint.config(
         },
       ],
 
+      'unicorn/no-null': 'off',
+
+      '@typescript-eslint/no-unsafe-argument': 'off',
+      '@typescript-eslint/no-unsafe-return': 'off',
+      '@typescript-eslint/no-unsafe-call': 'off',
       '@typescript-eslint/no-non-null-assertion': 'off',
       '@typescript-eslint/ban-ts-comment': 'off',
       '@typescript-eslint/no-unsafe-assignment': 'off',

package.json

@@ -28,7 +28,7 @@
     "format": "prettier --write .",
     "build": "tsc && NODE_ENV=production node esbuild.mjs",
     "prebuild": "npm run clean",
-    "lint": "eslint --report-unused-disable-directives --max-warnings 0 src/",
+    "lint": "eslint --report-unused-disable-directives --max-warnings 0",
     "prepack": "npm run build",
     "postversion": "git push --follow-tags"
   },

src/LaunchMsaView/components/LaunchMsaViewDialog.tsx

@@ -5,9 +5,10 @@ import { AbstractTrackModel, Feature } from '@jbrowse/core/util'
 
 // locals
 
-import { CustomTabPanel, a11yProps } from './TabUtils'
+import CustomTabPanel from './TabUtils'
 import NewNcbiBlastQueryPanel from './NewNCBIBlastQuery'
 import PreLoadedMSA from './PreLoadedMSA/PreLoadedMSADataPanel'
+import { a11yProps } from './tabUtil'
 
 export default function LaunchProteinViewDialog({
   handleClose,

src/LaunchMsaView/components/NewNCBIBlastQuery/useFeatureSequence.ts

@@ -39,7 +39,7 @@ export function useFeatureSequence({
           throw new Error('assembly not found')
         }
         const sessionId = 'getSequence'
-        const feats = await rpcManager.call(sessionId, 'CoreGetFeatures', {
+        const feats = (await rpcManager.call(sessionId, 'CoreGetFeatures', {
           adapterConfig: getConf(assembly, ['sequence', 'adapter']),
           sessionId,
           regions: [
@@ -50,19 +50,25 @@ export function useFeatureSequence({
               assemblyName,
             },
           ],
-        })
+        })) as Feature[]
 
-        const [feat] = feats as Feature[]
-        return (feat?.get('seq') as string | undefined) || ''
+        const res = (feats[0]?.get('seq') as string | undefined) ?? ''
+        if (!res) {
+          throw new Error('no sequence')
+        }
+        return res
       }
 
       // eslint-disable-next-line @typescript-eslint/no-floating-promises
       ;(async () => {
         try {
           setError(undefined)
           setSequence(undefined)
-          // eslint-disable-next-line @typescript-eslint/no-explicit-any
-          const { start, end, refName } = feature.toJSON() as any
+          const { start, end, refName } = feature.toJSON() as {
+            start: number
+            end: number
+            refName: string
+          }
 
           if (!forceLoad && end - start > BPLIMIT) {
             setSequence({

src/LaunchMsaView/components/TabUtils.tsx

@@ -7,7 +7,7 @@ interface TabPanelProps {
   value: number
 }
 
-export function CustomTabPanel(props: TabPanelProps) {
+export default function CustomTabPanel(props: TabPanelProps) {
   const { children, value, index, ...other } = props
 
   return (
@@ -22,9 +22,3 @@ export function CustomTabPanel(props: TabPanelProps) {
     </div>
   )
 }
-export function a11yProps(index: number) {
-  return {
-    id: `gtab-${index}`,
-    'aria-controls': `gtabpanel-${index}`,
-  }
-}

src/LaunchMsaView/components/tabUtil.ts

@@ -0,0 +1,6 @@
+export function a11yProps(index: number) {
+  return {
+    id: `gtab-${index}`,
+    'aria-controls': `gtabpanel-${index}`,
+  }
+}

src/LaunchMsaView/index.ts

@@ -2,50 +2,55 @@ import PluginManager from '@jbrowse/core/PluginManager'
 import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'
 import { PluggableElementType } from '@jbrowse/core/pluggableElementTypes'
 import { IAnyModelType } from 'mobx-state-tree'
-import { getSession, getContainingTrack } from '@jbrowse/core/util'
+import { getSession, getContainingTrack, Feature } from '@jbrowse/core/util'
 
 // icons
 import AddIcon from '@mui/icons-material/Add'
 
 // locals
 import LaunchMsaViewDialog from './components/LaunchMsaViewDialog'
+import { MenuItem } from '@jbrowse/core/ui'
 
 function isDisplay(elt: { name: string }): elt is DisplayType {
   return elt.name === 'LinearBasicDisplay'
 }
 
 function extendStateModel(stateModel: IAnyModelType) {
-  return stateModel.views(self => {
-    const superContextMenuItems = self.contextMenuItems
-    return {
-      contextMenuItems() {
-        const feature = self.contextMenuFeature
-        const track = getContainingTrack(self)
-        return [
-          ...superContextMenuItems(),
-          ...(feature
-            ? [
-                {
-                  label: 'Launch MSA view',
-                  icon: AddIcon,
-                  onClick: () => {
-                    const session = getSession(track)
-                    session.queueDialog(handleClose => [
-                      LaunchMsaViewDialog,
-                      {
-                        model: track,
-                        handleClose,
-                        feature,
-                      },
-                    ])
+  return stateModel.views(
+    (self: {
+      contextMenuItems: () => MenuItem[]
+      contextMenuFeature?: Feature
+    }) => {
+      const superContextMenuItems = self.contextMenuItems
+      return {
+        contextMenuItems() {
+          const feature = self.contextMenuFeature
+          const track = getContainingTrack(self)
+          return [
+            ...superContextMenuItems(),
+            ...(feature
+              ? [
+                  {
+                    label: 'Launch MSA view',
+                    icon: AddIcon,
+                    onClick: () => {
+                      getSession(track).queueDialog(handleClose => [
+                        LaunchMsaViewDialog,
+                        {
+                          model: track,
+                          handleClose,
+                          feature,
+                        },
+                      ])
+                    },
                   },
-                },
-              ]
-            : []),
-        ]
-      },
-    }
-  })
+                ]
+              : []),
+          ]
+        },
+      }
+    },
+  )
 }
 
 export default function LaunchMsaViewF(pluginManager: PluginManager) {

src/LaunchMsaView/util.ts

@@ -11,8 +11,8 @@ export function getTranscriptFeatures(feature: Feature) {
         f.get('subfeatures')?.some(f => f.get('type') === 'CDS'),
       )
 }
-export function getId(val?: Feature) {
-  return val === undefined ? '' : val.get('name') || val.get('id')
+export function getId(val?: Feature): string {
+  return val?.get('name') || val?.get('id') || ''
 }
 
 export function getTranscriptDisplayName(val?: Feature) {

src/MsaViewPanel/msaCoordToGenomeCoord.ts

@@ -9,7 +9,7 @@ export function msaCoordToGenomeCoord({
   coord: number
 }) {
   const { transcriptToMsaMap } = model
-  if (mouseCol === undefined || transcriptToMsaMap === undefined) {
+  if (transcriptToMsaMap === undefined) {
     return
   }
 

src/utils/msa.ts

@@ -98,6 +98,7 @@ async function wait({
   algorithm: string
   onProgress: (arg: string) => void
 }) {
+  // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
   while (true) {
     for (let i = 0; i < 10; i++) {
       await timeout(1000)
@@ -107,6 +108,8 @@ async function wait({
 
     if (result === 'FINISHED') {
       break
+    } else if (result.includes('FAILURE')) {
+      throw new Error(`Failed to run: jobId ${jobId}`)
     }
   }
 }

src/utils/ncbiBlast.ts

@@ -23,15 +23,26 @@ export async function queryBlast({
   })
   onRid(rid)
   await waitForRid({ rid, onProgress })
-  const ret = await jsonfetch(
+  const ret = (await jsonfetch(
     `${BLAST_URL}?CMD=Get&RID=${rid}&FORMAT_TYPE=JSON2_S&FORMAT_OBJECT=Alignment`,
-  )
-  const hits = ret.BlastOutput2[0].report.results.search.hits as {
-    description: { accession: string; id: string; sciname: string }[]
-    hsps: { hseq: string }[]
-  }[]
-
-  return { rid, hits }
+  )) as {
+    BlastOutput2: {
+      report: {
+        results: {
+          search: {
+            hits: {
+              description: { accession: string; id: string; sciname: string }[]
+              hsps: { hseq: string }[]
+            }[]
+          }
+        }
+      }
+    }[]
+  }
+  return {
+    rid,
+    hits: ret.BlastOutput2[0]?.report.results.search.hits ?? [],
+  }
 }
 
 async function initialQuery({
@@ -78,6 +89,7 @@ async function waitForRid({
   rid: string
   onProgress: (arg: string) => void
 }) {
+  // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
   while (true) {
     const iter = 20
     for (let i = 0; i < iter; i++) {