@apollo-annotation/jbrowse-plugin-apollo 0.1.5 → 0.1.7

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@apollo-annotation/jbrowse-plugin-apollo",
-  "version": "0.1.5",
+  "version": "0.1.7",
   "description": "Apollo plugin for JBrowse 2",
   "repository": {
     "type": "git",
@@ -32,9 +32,9 @@
     "clean": "rimraf dist",
     "start": "yarn clean && npm-run-all --parallel start:watch start:server",
     "start:watch": "JB_NPM=false NODE_ENV=development rollup --config --watch",
-    "start:server": "serve --no-request-logging --cors --listen 9000 .",
+    "start:server": "serve --no-request-logging --cors --listen 9000 --no-port-switching .",
     "build": "yarn build:shared && yarn clean && rollup --config",
-    "browse": "serve --no-request-logging --listen 8999 .jbrowse",
+    "browse": "serve --no-request-logging --listen 8999 --no-port-switching .jbrowse",
     "test": "jest",
     "test:ci": "jest --coverage",
     "start:collab-cypress": "yarn workspace apollo-collaboration-server run cypress:start",
@@ -51,9 +51,9 @@
     "name": "Apollo"
   },
   "dependencies": {
-    "@apollo-annotation/apollo-common": "^0.1.5",
-    "@apollo-annotation/apollo-mst": "^0.1.5",
-    "@apollo-annotation/apollo-shared": "^0.1.5",
+    "@apollo-annotation/apollo-common": "^0.1.7",
+    "@apollo-annotation/apollo-mst": "^0.1.7",
+    "@apollo-annotation/apollo-shared": "^0.1.7",
     "@emotion/react": "^11.10.6",
     "@emotion/styled": "^11.10.6",
     "@gmod/gff": "1.2.0",

package/src/ApolloInternetAccount/addMenuItems.ts

@@ -54,8 +54,7 @@ export function addMenuItems(rootModel: AbstractMenuManager) {
             handleClose: () => {
               doneCallback()
             },
-            changeManager: (session as ApolloSessionModel).apolloDataStore
-              .changeManager,
+            changeManager: session.apolloDataStore.changeManager,
           },
         ],
       )
@@ -72,8 +71,7 @@ export function addMenuItems(rootModel: AbstractMenuManager) {
             handleClose: () => {
               doneCallback()
             },
-            changeManager: (session as ApolloSessionModel).apolloDataStore
-              .changeManager,
+            changeManager: session.apolloDataStore.changeManager,
           },
         ],
       )

package/src/ApolloInternetAccount/components/AuthTypeSelector.tsx

@@ -49,9 +49,9 @@ export const AuthTypeSelector = ({
       const data = (await response.json()) as string[]
       setLoginTypes(data)
     }
-    getAuthTypes().catch((error) =>
-      isAbortException(error) ? '' : setErrorMessage(String(error)),
-    )
+    getAuthTypes().catch((error) => {
+      isAbortException(error) ? '' : setErrorMessage(String(error))
+    })
     return () => {
       controller.abort()
     }
@@ -84,19 +84,27 @@ export const AuthTypeSelector = ({
         {allowGoogle ? (
           <GoogleButton
             disabled={!allowGoogle}
-            onClick={() => handleClick('google')}
+            onClick={() => {
+              handleClick('google')
+            }}
           />
         ) : null}
         {allowMicrosoft ? (
           <MicrosoftButton
             disabled={!allowMicrosoft}
-            onClick={() => handleClick('microsoft')}
+            onClick={() => {
+              handleClick('microsoft')
+            }}
           />
         ) : null}
         {allowGuest ? (
           <>
             <Divider className={classes.divider} />
-            <GuestButton onClick={() => handleClick('guest')} />
+            <GuestButton
+              onClick={() => {
+                handleClick('guest')
+              }}
+            />
           </>
         ) : null}
       </DialogContent>

package/src/ApolloInternetAccount/model.ts

@@ -1,3 +1,11 @@
+/* eslint-disable @typescript-eslint/no-unused-vars */
+/* eslint-disable @typescript-eslint/no-unsafe-return */
+/* eslint-disable @typescript-eslint/no-unsafe-member-access */
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
+/* eslint-disable @typescript-eslint/no-unsafe-call */
+/* eslint-disable @typescript-eslint/no-unsafe-argument */
+/* eslint-disable @typescript-eslint/unbound-method */
+/* eslint-disable @typescript-eslint/no-misused-promises */
 import { Change } from '@apollo-annotation/apollo-common'
 import {
   ChangeMessage,
@@ -88,8 +96,6 @@ const stateModelFactory = (configSchema: ApolloInternetAccountConfigModel) => {
           reject: (error: Error) => void,
         ) {
           listener = (event) => {
-            // this should probably get better handling, but ignored for now
-            // eslint-disable-next-line @typescript-eslint/no-floating-promises
             this.finishOAuthWindow(event, resolve, reject)
           }
           window.addEventListener('message', listener)
@@ -97,7 +103,7 @@ const stateModelFactory = (configSchema: ApolloInternetAccountConfigModel) => {
         deleteMessageChannel() {
           window.removeEventListener('message', listener)
         },
-        async finishOAuthWindow(
+        finishOAuthWindow(
           event: MessageEvent,
           resolve: (token: string) => void,
           reject: (error: Error) => void,
@@ -105,7 +111,8 @@ const stateModelFactory = (configSchema: ApolloInternetAccountConfigModel) => {
           if (
             event.data.name !== `JBrowseAuthWindow-${self.internetAccountId}`
           ) {
-            return this.deleteMessageChannel()
+            this.deleteMessageChannel()
+            return
           }
           const redirectUriWithInfo = event.data.redirectUri
           const fixedQueryString = redirectUriWithInfo.replace('#', '?')
@@ -115,11 +122,12 @@ const stateModelFactory = (configSchema: ApolloInternetAccountConfigModel) => {
           const token = urlParams.get('access_token')
           this.deleteMessageChannel()
           if (!token) {
-            return reject(new Error('Error with token endpoint'))
+            reject(new Error('Error with token endpoint'))
+            return
           }
           self.storeToken(token)
           self.setRole()
-          return resolve(token)
+          resolve(token)
         },
         async openAuthWindow(
           type: string,
@@ -149,7 +157,6 @@ const stateModelFactory = (configSchema: ApolloInternetAccountConfigModel) => {
             const eventFromDesktop = new MessageEvent('message', {
               data: { name: eventName, redirectUri: redirectUriFromElectron },
             })
-            // eslint-disable-next-line @typescript-eslint/no-floating-promises
             this.finishOAuthWindow(eventFromDesktop, resolve, reject)
           } else {
             this.addMessageChannel(resolve, reject)
@@ -204,7 +211,8 @@ const stateModelFactory = (configSchema: ApolloInternetAccountConfigModel) => {
             response,
             'Error when logging in',
           )
-          return reject(new Error(errorMessage))
+          reject(new Error(errorMessage))
+          return
         }
         const { token } = await response.json()
         resolve(token)
@@ -246,8 +254,7 @@ const stateModelFactory = (configSchema: ApolloInternetAccountConfigModel) => {
       ),
       getMissingChanges: flow(function* getMissingChanges() {
         const { session } = getRoot<ApolloRootModel>(self)
-        const { changeManager } = (session as ApolloSessionModel)
-          .apolloDataStore
+        const { changeManager } = session.apolloDataStore
         if (!self.lastChangeSequenceNumber) {
           throw new Error(
             'No LastChangeSequence stored in session. Please, refresh you browser to get last updates from server',
@@ -277,7 +284,7 @@ const stateModelFactory = (configSchema: ApolloInternetAccountConfigModel) => {
         const serializedChanges = yield response.json()
         for (const serializedChange of serializedChanges) {
           const change = Change.fromJSON(serializedChange)
-          void changeManager?.submit(change, { submitToBackend: false })
+          void changeManager.submit(change, { submitToBackend: false })
         }
       }),
     }))
@@ -293,9 +300,8 @@ const stateModelFactory = (configSchema: ApolloInternetAccountConfigModel) => {
           throw new Error('No Token found')
         }
         const { socket } = self
-        const { addCheckResult, changeManager, deleteCheckResult } = (
-          session as ApolloSessionModel
-        ).apolloDataStore
+        const { addCheckResult, changeManager, deleteCheckResult } =
+          session.apolloDataStore
         socket.on('connect', async () => {
           await self.getMissingChanges()
         })
@@ -320,7 +326,7 @@ const stateModelFactory = (configSchema: ApolloInternetAccountConfigModel) => {
             return // we did this change, no need to apply it again
           }
           const change = Change.fromJSON(message.changeInfo)
-          void changeManager?.submit(change, { submitToBackend: false })
+          void changeManager.submit(change, { submitToBackend: false })
         })
         socket.on('USER_LOCATION', (message: UserLocationMessage) => {
           const { channel, locations, userName, userSessionId } = message
@@ -380,7 +386,9 @@ const stateModelFactory = (configSchema: ApolloInternetAccountConfigModel) => {
         let timeoutId: ReturnType<typeof setTimeout>
         return (userLocation: UserLocation[]) => {
           clearTimeout(timeoutId)
-          timeoutId = setTimeout(() => fn(userLocation), debounceTimeout)
+          timeoutId = setTimeout(() => {
+            fn(userLocation)
+          }, debounceTimeout)
         }
       }
       return { postUserLocation: debouncePostUserLocation(postUserLocation) }

package/src/ApolloJobModel.ts

@@ -1,3 +1,5 @@
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
+/* eslint-disable @typescript-eslint/no-confusing-void-expression */
 import {
   SessionWithWidgets,
   getSession,

package/src/ApolloSequenceAdapter/ApolloSequenceAdapter.ts

@@ -1,3 +1,7 @@
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
+/* eslint-disable @typescript-eslint/no-unsafe-argument */
+/* eslint-disable @typescript-eslint/no-unsafe-member-access */
+/* eslint-disable @typescript-eslint/no-unsafe-call */
 import { readConfObject } from '@jbrowse/core/configuration'
 import {
   BaseOptions,

package/src/ApolloSixFrameRenderer/ApolloSixFrameRenderer.tsx

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/require-await */
 import { RenderProps, RendererType } from '@jbrowse/core/pluggableElementTypes'
 import RpcManager from '@jbrowse/core/rpc/RpcManager'
 

package/src/ApolloSixFrameRenderer/components/ApolloRendering.tsx

@@ -1,3 +1,10 @@
+/* eslint-disable react-hooks/exhaustive-deps */
+/* eslint-disable @typescript-eslint/unbound-method */
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
+/* eslint-disable @typescript-eslint/no-unsafe-call */
+/* eslint-disable @typescript-eslint/no-unsafe-argument */
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
+/* eslint-disable @typescript-eslint/no-misused-promises */
 import { AnnotationFeatureI } from '@apollo-annotation/apollo-mst'
 import {
   LocationEndChange,
@@ -93,8 +100,14 @@ function ApolloRendering(props: ApolloRenderingProps) {
   const { collaborators: collabs } = session
 
   // bridging mobx observability and React useEffect observability
-  // eslint-disable-next-line react-hooks/exhaustive-deps
-  useEffect(() => autorun(() => setCollaborators(toJS(collabs))), [])
+
+  useEffect(
+    () =>
+      autorun(() => {
+        setCollaborators(toJS(collabs))
+      }),
+    [],
+  )
 
   const [region] = regions
   const totalWidth = (region.end - region.start) / bpPerPx
@@ -536,7 +549,7 @@ function ApolloRendering(props: ApolloRenderingProps) {
           assembly,
         })
       }
-      await changeManager?.submit(change)
+      await changeManager.submit(change)
     }
     // eslint-disable-next-line unicorn/no-useless-undefined
     setDragging(undefined)

package/src/ApolloTextSearchAdapter/ApolloTextSearchAdapter.ts

@@ -1,3 +1,8 @@
+/* eslint-disable @typescript-eslint/no-unsafe-return */
+/* eslint-disable @typescript-eslint/no-unsafe-member-access */
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
+/* eslint-disable @typescript-eslint/no-unsafe-call */
+/* eslint-disable @typescript-eslint/no-unsafe-argument */
 import { readConfObject } from '@jbrowse/core/configuration'
 import {
   BaseAdapter,

package/src/BackendDrivers/CollaborationServerDriver.ts

@@ -1,3 +1,9 @@
+/* eslint-disable @typescript-eslint/no-base-to-string */
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
+/* eslint-disable @typescript-eslint/no-unsafe-return */
+/* eslint-disable @typescript-eslint/no-unsafe-member-access */
+/* eslint-disable @typescript-eslint/no-unsafe-call */
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import {
   AssemblySpecificChange,
   Change,
@@ -108,7 +114,7 @@ export class CollaborationServerDriver extends BackendDriver {
       )
       throw new Error(errorMessage)
     }
-    await this.checkSocket(assemblyName, refName, internetAccount)
+    this.checkSocket(assemblyName, refName, internetAccount)
     return response.json() as Promise<
       [AnnotationFeatureSnapshot[], CheckResultSnapshot[]]
     >
@@ -120,7 +126,7 @@ export class CollaborationServerDriver extends BackendDriver {
    * @param refSeq - refSeqName
    * @param internetAccount - internet account
    */
-  async checkSocket(
+  checkSocket(
     assembly: string,
     refSeq: string,
     internetAccount: ApolloInternetAccount,
@@ -173,7 +179,7 @@ export class CollaborationServerDriver extends BackendDriver {
     if (!apolloAssembly) {
       apolloAssembly = this.clientStore.addAssembly(assemblyName)
     }
-    let apolloRefSeq = apolloAssembly?.refSeqs.get(refSeq)
+    let apolloRefSeq = apolloAssembly.refSeqs.get(refSeq)
     if (!apolloRefSeq) {
       apolloRefSeq = apolloAssembly.addRefSeq(refSeq, refName)
     }
@@ -204,7 +210,7 @@ export class CollaborationServerDriver extends BackendDriver {
     )
     this.inFlight.set(inFlightKey, seqPromise)
     const seq = await seqPromise
-    await this.checkSocket(assemblyName, refName, internetAccount)
+    this.checkSocket(assemblyName, refName, internetAccount)
     this.inFlight.delete(inFlightKey)
     return { seq, refSeq }
   }

package/src/BackendDrivers/DesktopFileDriver.ts

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/require-await */
 import {
   AssemblySpecificChange,
   Change,

package/src/BackendDrivers/InMemoryFileDriver.ts

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/require-await */
 import {
   AssemblySpecificChange,
   Change,

package/src/ChangeManager.ts

@@ -1,3 +1,6 @@
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
+/* eslint-disable @typescript-eslint/no-unsafe-call */
+/* eslint-disable @typescript-eslint/no-unsafe-member-access */
 import {
   Change,
   ClientDataStore,

package/src/FeatureDetailsWidget/Attributes.tsx

@@ -1,3 +1,6 @@
+/* eslint-disable @typescript-eslint/unbound-method */
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
+/* eslint-disable @typescript-eslint/no-misused-promises */
 import { AnnotationFeatureI } from '@apollo-annotation/apollo-mst'
 import { FeatureAttributeChange } from '@apollo-annotation/apollo-shared'
 import { AbstractSessionModel } from '@jbrowse/core/util'
@@ -190,7 +193,7 @@ export const Attributes = observer(function Attributes({
       featureId: feature._id,
       attributes: attrs,
     })
-    await changeManager.submit?.(change)
+    await changeManager.submit(change)
     notify('Feature attributes modified successfully', 'success')
   }
   function handleAddNewAttributeChange() {

package/src/FeatureDetailsWidget/BasicInformation.tsx

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/no-misused-promises */
 import { AnnotationFeatureI } from '@apollo-annotation/apollo-mst'
 import {
   LocationEndChange,
@@ -39,8 +40,9 @@ export const BasicInformation = observer(function BasicInformation({
 
   const { _id, assemblyId, end, start, strand, type } = feature
 
-  const notifyError = (e: Error) =>
-    (session as unknown as AbstractSessionModel).notify(e.message, 'error')
+  const notifyError = (e: Error) => {
+    ;(session as unknown as AbstractSessionModel).notify(e.message, 'error')
+  }
 
   const { changeManager } = session.apolloDataStore
   function handleTypeChange(newType: string) {

package/src/FeatureDetailsWidget/NumberTextField.tsx

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/no-unsafe-argument */
 import { TextField, TextFieldProps } from '@mui/material'
 import { observer } from 'mobx-react'
 import React, { useEffect, useState } from 'react'
@@ -67,7 +68,9 @@ export const NumberTextField = observer(function NumberTextField({
           }
         }
       }}
-      inputRef={(node) => setInputNode(node)}
+      inputRef={(node) => {
+        setInputNode(node)
+      }}
       error={error}
       helperText={error ? 'Not a valid number' : undefined}
     />

package/src/FeatureDetailsWidget/RelatedFeature.tsx

@@ -1,3 +1,6 @@
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
+/* eslint-disable @typescript-eslint/no-unsafe-member-access */
+/* eslint-disable @typescript-eslint/no-unsafe-argument */
 import {
   AnnotationFeature,
   AnnotationFeatureI,
@@ -46,7 +49,7 @@ export const RelatedFeatures = observer(function RelatedFeatures({
         assembly,
         refName,
       })
-      ;(session as unknown as SessionWithWidgets).showWidget?.(
+      ;(session as unknown as SessionWithWidgets).showWidget(
         apolloFeatureWidget,
       )
     }
@@ -63,7 +66,12 @@ export const RelatedFeatures = observer(function RelatedFeatures({
           <Typography variant="h5">Parent</Typography>
           <Paper elevation={6} className={classes.paper}>
             {`Start: ${parent.start}, End: ${parent.end}, Type: ${parent.type}`}
-            <Button variant="contained" onClick={() => onButtonClick(parent)}>
+            <Button
+              variant="contained"
+              onClick={() => {
+                onButtonClick(parent)
+              }}
+            >
               Go to parent
             </Button>
           </Paper>
@@ -75,7 +83,12 @@ export const RelatedFeatures = observer(function RelatedFeatures({
           {[...children.values()].map((child) => (
             <Paper elevation={6} className={classes.paper} key={child._id}>
               {`Start: ${child.start}, End: ${child.end}, Type: ${child.type}`}
-              <Button variant="contained" onClick={() => onButtonClick(child)}>
+              <Button
+                variant="contained"
+                onClick={() => {
+                  onButtonClick(child)
+                }}
+              >
                 Go to child
               </Button>
             </Paper>

package/src/FeatureDetailsWidget/Sequence.tsx

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import { AnnotationFeatureI } from '@apollo-annotation/apollo-mst'
 import { splitStringIntoChunks } from '@apollo-annotation/apollo-shared'
 import { Button, Typography } from '@mui/material'

package/src/FeatureDetailsWidget/StringTextField.tsx

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/no-unsafe-argument */
 import { TextField, TextFieldProps } from '@mui/material'
 import { observer } from 'mobx-react'
 import React, { useEffect, useState } from 'react'
@@ -54,7 +55,9 @@ export const StringTextField = observer(function StringTextField({
           onChangeCommitted(value)
         }
       }}
-      inputRef={(node) => setInputNode(node)}
+      inputRef={(node) => {
+        setInputNode(node)
+      }}
     />
   )
 })

package/src/FeatureDetailsWidget/model.ts

@@ -1,3 +1,5 @@
+/* eslint-disable @typescript-eslint/no-unsafe-call */
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import {
   AnnotationFeature,
   AnnotationFeatureI,

package/src/LinearApolloDisplay/components/LinearApolloDisplay.tsx

@@ -1,3 +1,8 @@
+/* eslint-disable @typescript-eslint/unbound-method */
+/* eslint-disable @typescript-eslint/no-misused-promises */
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
+/* eslint-disable @typescript-eslint/no-unsafe-argument */
 import { Menu, MenuItem } from '@jbrowse/core/ui'
 import {
   AbstractSessionModel,
@@ -66,7 +71,9 @@ export const LinearApolloDisplay = observer(function LinearApolloDisplay(
   const { classes } = useStyles()
   const lgv = getContainingView(model) as unknown as LinearGenomeViewModel
 
-  useEffect(() => setTheme(theme), [theme, setTheme])
+  useEffect(() => {
+    setTheme(theme)
+  }, [theme, setTheme])
   const [contextCoord, setContextCoord] = useState<Coord>()
   const [contextMenuItems, setContextMenuItems] = useState<MenuItem[]>([])
   const message = regionCannotBeRendered()
@@ -178,7 +185,7 @@ export const LinearApolloDisplay = observer(function LinearApolloDisplay(
                 .filter(
                   (checkResult) =>
                     assembly?.isValidRefName(checkResult.refSeq) &&
-                    assembly?.getCanonicalRefName(checkResult.refSeq) ===
+                    assembly.getCanonicalRefName(checkResult.refSeq) ===
                       region.refName &&
                     doesIntersect2(
                       region.start,

package/src/LinearApolloDisplay/glyphs/BoxGlyph.ts

@@ -1,3 +1,5 @@
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
+/* eslint-disable @typescript-eslint/unbound-method */
 import { AnnotationFeatureI } from '@apollo-annotation/apollo-mst'
 import {
   LocationEndChange,

package/src/LinearApolloDisplay/glyphs/CanonicalGeneGlyph.ts

@@ -1,3 +1,8 @@
+/* eslint-disable @typescript-eslint/no-unsafe-member-access */
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
+/* eslint-disable @typescript-eslint/no-unsafe-argument */
+/* eslint-disable @typescript-eslint/unbound-method */
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import { AnnotationFeatureI } from '@apollo-annotation/apollo-mst'
 import {
   DiscontinuousLocationEndChange,
@@ -301,7 +306,7 @@ export class CanonicalGeneGlyph extends Glyph {
         let featureRow: number | undefined
         let i = 0
         for (const [, f] of children ?? new Map()) {
-          if (f._id === apolloSelectedFeature?._id) {
+          if (f._id === apolloSelectedFeature._id) {
             featureEntry = f
             featureRow = i
           }
@@ -412,7 +417,7 @@ export class CanonicalGeneGlyph extends Glyph {
     let featureRow: number | undefined
     let i = 0
     for (const [, f] of topLevelFeature.children ?? new Map()) {
-      if (f._id === feature?._id) {
+      if (f._id === feature._id) {
         featureEntry = f
         featureRow = i
       }
@@ -874,10 +879,10 @@ export class CanonicalGeneGlyph extends Glyph {
 
     if (feature.type !== 'CDS') {
       const adjacentExons = this.adjacentExonsOfExon(feature, topLevelFeature)
-      if (adjacentExons?.nextExon && bp >= adjacentExons?.nextExon.start - 1) {
+      if (adjacentExons?.nextExon && bp >= adjacentExons.nextExon.start - 1) {
         return
       }
-      if (adjacentExons?.prevExon && bp <= adjacentExons?.prevExon.end + 1) {
+      if (adjacentExons?.prevExon && bp <= adjacentExons.prevExon.end + 1) {
         return
       }
       const dls: CDSDiscontinuousLocation[] = this.cdsDlsForExon(

package/src/LinearApolloDisplay/glyphs/GenericChildGlyph.ts

@@ -1,3 +1,6 @@
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
+/* eslint-disable @typescript-eslint/no-unsafe-argument */
+/* eslint-disable @typescript-eslint/unbound-method */
 import { AnnotationFeatureI } from '@apollo-annotation/apollo-mst'
 
 import { LinearApolloDisplay } from '../stateModel'
@@ -133,7 +136,7 @@ export class GenericChildGlyph extends BoxGlyph {
 
   getFeatureFromLayout(feature: AnnotationFeatureI, bp: number, row: number) {
     const layoutRow = this.featuresForRow(feature)[row]
-    return layoutRow?.find((f) => bp >= f.start && bp <= f.end)
+    return layoutRow.find((f) => bp >= f.start && bp <= f.end)
   }
 
   getRowForFeature(

package/src/LinearApolloDisplay/glyphs/Glyph.ts

@@ -1,3 +1,7 @@
+/* eslint-disable @typescript-eslint/unbound-method */
+/* eslint-disable @typescript-eslint/no-unsafe-member-access */
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
+/* eslint-disable @typescript-eslint/no-unsafe-return */
 import { AnnotationFeatureI } from '@apollo-annotation/apollo-mst'
 import { MenuItem } from '@jbrowse/core/ui'
 import { AbstractSessionModel, SessionWithWidgets } from '@jbrowse/core/util'
@@ -389,7 +393,7 @@ export abstract class Glyph {
                 refName: region.refName,
               },
             )
-            ;(session as unknown as SessionWithWidgets).showWidget?.(
+            ;(session as unknown as SessionWithWidgets).showWidget(
               apolloFeatureWidget,
             )
           },

package/src/LinearApolloDisplay/glyphs/ImplicitExonGeneGlyph.ts

@@ -1,3 +1,9 @@
+/* eslint-disable @typescript-eslint/no-unsafe-member-access */
+/* eslint-disable @typescript-eslint/no-unsafe-argument */
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
+/* eslint-disable @typescript-eslint/no-unsafe-call */
+/* eslint-disable @typescript-eslint/unbound-method */
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import { AnnotationFeatureI } from '@apollo-annotation/apollo-mst'
 import {
   LocationEndChange,
@@ -187,7 +193,7 @@ export class ImplicitExonGeneGlyph extends Glyph {
         let featureRow: number | undefined
         let i = 0
         for (const [, f] of children ?? new Map()) {
-          if (f._id === apolloSelectedFeature?._id) {
+          if (f._id === apolloSelectedFeature._id) {
             featureEntry = f
             featureRow = i
           }
@@ -541,7 +547,7 @@ export class ImplicitExonGeneGlyph extends Glyph {
     row: number,
   ): AnnotationFeatureI | undefined {
     const layoutRow = this.featuresForRow(feature)[row]
-    return layoutRow?.find((f) => bp >= f.start && bp <= f.end)
+    return layoutRow.find((f) => bp >= f.start && bp <= f.end)
   }
 
   getRowForFeature(

package/src/LinearApolloDisplay/stateModel/base.ts

@@ -1,3 +1,8 @@
+/* eslint-disable @typescript-eslint/unbound-method */
+/* eslint-disable @typescript-eslint/no-unsafe-return */
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
+/* eslint-disable @typescript-eslint/no-unsafe-member-access */
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import { AnnotationFeatureI } from '@apollo-annotation/apollo-mst'
 import { ConfigurationReference, getConf } from '@jbrowse/core/configuration'
 import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
@@ -101,7 +106,7 @@ export function baseModelFactory(
       },
       get changeManager() {
         return (self.session as unknown as ApolloSessionModel).apolloDataStore
-          ?.changeManager
+          .changeManager
       },
       getAssemblyId(assemblyName: string) {
         const { assemblyManager } =
@@ -119,7 +124,7 @@ export function baseModelFactory(
     }))
     .actions((self) => ({
       setSelectedFeature(feature?: AnnotationFeatureI) {
-        return (
+        ;(
           self.session as unknown as ApolloSessionModel
         ).apolloSetSelectedFeature(feature)
       },

package/src/LinearApolloDisplay/stateModel/getGlyph.ts

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/no-unsafe-member-access */
 import { AnnotationFeatureI } from '@apollo-annotation/apollo-mst'
 
 import {