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/AddHighlightModel/MsaToGenomeHighlight.tsx

@@ -22,11 +22,13 @@ const MsaToGenomeHighlight = observer(function MsaToGenomeHighlight2({
 }) {
   const { classes } = useStyles()
   const { assemblyManager, views } = getSession(model)
-  const p = views.find(f => f.type === 'MsaView') as JBrowsePluginMsaViewModel
+  const p = views.find(f => f.type === 'MsaView') as
+    | JBrowsePluginMsaViewModel
+    | undefined
   const assembly = assemblyManager.get(model.assemblyNames[0]!)
   return assembly ? (
     <>
-      {p.connectedHighlights.map((r, idx) => {
+      {p?.connectedHighlights.map((r, idx) => {
         const refName = getCanonicalName(assembly, r.refName)
         const s = model.bpToPx({ refName, coord: r.start })
         const e = model.bpToPx({ refName, coord: r.end })

src/AddHighlightModel/util.ts

@@ -6,7 +6,7 @@ export const useStyles = makeStyles()({
     background: 'rgba(255,255,0,0.2)',
     border: '1px solid rgba(50,50,0,0.2)',
     position: 'absolute',
-    zIndex: 1000,
+    zIndex: 99,
     textAlign: 'center',
     pointerEvents: 'none',
     overflow: 'hidden',

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

@@ -1,6 +1,6 @@
 import { useEffect, useState } from 'react'
 
-import { Feature, getSession } from '@jbrowse/core/util'
+import { AbstractSessionModel, Feature, getSession } from '@jbrowse/core/util'
 import { getConf } from '@jbrowse/core/configuration'
 
 export interface SeqState {
@@ -14,6 +14,40 @@ export interface ErrorState {
 }
 const BPLIMIT = 500_000
 
+async function fetchSeq({
+  start,
+  end,
+  refName,
+  session,
+  assemblyName,
+}: {
+  start: number
+  end: number
+  refName: string
+  assemblyName: string
+  session: AbstractSessionModel
+}) {
+  const { assemblyManager, rpcManager } = session
+  const assembly = await assemblyManager.waitForAssembly(assemblyName)
+  if (!assembly) {
+    throw new Error('assembly not found')
+  }
+  const sessionId = 'getSequence'
+  const feats = (await rpcManager.call(sessionId, 'CoreGetFeatures', {
+    adapterConfig: getConf(assembly, ['sequence', 'adapter']),
+    sessionId,
+    regions: [
+      {
+        start,
+        end,
+        refName: assembly.getCanonicalRefName(refName),
+        assemblyName,
+      },
+    ],
+  })) as Feature[]
+  return (feats[0]?.get('seq') as string | undefined) ?? ''
+}
+
 export function useFeatureSequence({
   view,
   feature,
@@ -27,61 +61,60 @@ export function useFeatureSequence({
 }) {
   const [sequence, setSequence] = useState<SeqState | ErrorState>()
   const [error, setError] = useState<unknown>()
+  const assemblyName = view?.assemblyNames?.[0]
   useEffect(() => {
     if (view) {
-      const { assemblyManager, rpcManager } = getSession(view)
-      const assemblyName = view.assemblyNames?.[0]
-      async function fetchSeq(start: number, end: number, refName: string) {
-        const assembly = assemblyName
-          ? await assemblyManager.waitForAssembly(assemblyName)
-          : undefined
-        if (!assembly) {
-          throw new Error('assembly not found')
-        }
-        const sessionId = 'getSequence'
-        const feats = await rpcManager.call(sessionId, 'CoreGetFeatures', {
-          adapterConfig: getConf(assembly, ['sequence', 'adapter']),
-          sessionId,
-          regions: [
-            {
-              start,
-              end,
-              refName: assembly.getCanonicalRefName(refName),
-              assemblyName,
-            },
-          ],
-        })
-
-        const [feat] = feats as Feature[]
-        return (feat?.get('seq') as string | undefined) || ''
-      }
-
       // 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 session = getSession(view)
+          const { start, end, refName } = feature.toJSON() as {
+            start: number
+            end: number
+            refName: string
+          }
+          if (!assemblyName) {
+            throw new Error('No assembly found')
+          }
           if (!forceLoad && end - start > BPLIMIT) {
             setSequence({
               error: `Genomic sequence larger than ${BPLIMIT}bp, use "force load" button to display`,
             })
           } else {
             const b = start - upDownBp
             const e = end + upDownBp
-            const seq = await fetchSeq(start, end, refName)
-            const up = await fetchSeq(Math.max(0, b), start, refName)
-            const down = await fetchSeq(end, e, refName)
-            setSequence({ seq, upstream: up, downstream: down })
+            setSequence({
+              seq: await fetchSeq({
+                start,
+                end,
+                refName,
+                assemblyName,
+                session,
+              }),
+              upstream: await fetchSeq({
+                start: Math.max(0, b),
+                end: start,
+                refName,
+                assemblyName,
+                session,
+              }),
+              downstream: await fetchSeq({
+                start: end,
+                end: e,
+                refName,
+                assemblyName,
+                session,
+              }),
+            })
           }
         } catch (e) {
           console.error(e)
           setError(e)
         }
       })()
     }
-  }, [feature, view, upDownBp, forceLoad])
+  }, [feature, view, upDownBp, assemblyName, forceLoad])
   return { sequence, error }
 }

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

@@ -9,13 +9,13 @@ export function msaCoordToGenomeCoord({
   coord: number
 }) {
   const { transcriptToMsaMap } = model
-  if (mouseCol === undefined || transcriptToMsaMap === undefined) {
+  if (transcriptToMsaMap === undefined) {
     return
   }
 
-  const c = mouseCol - 1
-  const k1 = model.globalCoordToRowSpecificSeqCoord('QUERY', c) || 0
-  const k2 = model.globalCoordToRowSpecificSeqCoord('QUERY', c + 1) || 0
+  const c = mouseCol
+  const k1 = model.seqCoordToRowSpecificGlobalCoord('QUERY', c) || 0
+  const k2 = model.seqCoordToRowSpecificGlobalCoord('QUERY', c + 1) || 0
   const { refName, p2g } = transcriptToMsaMap
   const s = p2g[k1]
   const e = p2g[k2]

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}`)
     }
   }
 }