@apollo-annotation/jbrowse-plugin-apollo 0.1.6 → 0.1.8

package/src/LinearApolloDisplay/stateModel/glyphs.ts

@@ -1,3 +1,5 @@
+/* eslint-disable @typescript-eslint/no-unsafe-argument */
+/* eslint-disable @typescript-eslint/no-unsafe-return */
 import { AnnotationFeatureI } from '@apollo-annotation/apollo-mst'
 import { ObservableMap, observable } from 'mobx'
 import { types } from 'mobx-state-tree'

package/src/LinearApolloDisplay/stateModel/layouts.ts

@@ -1,3 +1,6 @@
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
+/* eslint-disable @typescript-eslint/no-unsafe-argument */
+/* eslint-disable @typescript-eslint/no-unsafe-member-access */
 import { AnnotationFeatureI } from '@apollo-annotation/apollo-mst'
 import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
 import PluginManager from '@jbrowse/core/PluginManager'

package/src/LinearApolloDisplay/stateModel/mouseEvents.ts

@@ -1,3 +1,5 @@
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
+/* eslint-disable @typescript-eslint/no-unsafe-member-access */
 import { AnnotationFeatureI } from '@apollo-annotation/apollo-mst'
 import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
 import PluginManager from '@jbrowse/core/PluginManager'
@@ -193,7 +195,7 @@ export function mouseEventsSeqHightlightModelFactory(
       addDisposer(
         self,
         autorun(
-          async () => {
+          () => {
             if (!self.lgv.initialized || self.regionCannotBeRendered()) {
               return
             }

package/src/LinearApolloDisplay/stateModel/rendering.ts

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
 import PluginManager from '@jbrowse/core/PluginManager'
 import { defaultCodonTable, doesIntersect2, revcom } from '@jbrowse/core/util'
@@ -174,8 +175,8 @@ function codonColorCode(letter: string, rowColorCode: string, bpPerPx: number) {
     '*': '#f44336',
   }
 
-  if (colorMap[letter?.toUpperCase()] !== undefined) {
-    return colorMap[letter?.toUpperCase()]
+  if (colorMap[letter.toUpperCase()] !== undefined) {
+    return colorMap[letter.toUpperCase()]
   }
 
   return bpPerPx <= 0.1 ? rowColorCode : 'lightgray'

package/src/LinearApolloDisplay/types.ts

@@ -1 +1 @@
-export type CanvasMouseEvent = React.MouseEvent<HTMLCanvasElement, MouseEvent>
+export type CanvasMouseEvent = React.MouseEvent<HTMLCanvasElement>

package/src/OntologyManager/OntologyStore/fulltext.ts

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/no-unsafe-return */
 /* eslint-disable import/no-named-as-default-member */
 // jsonpath triggers this rule for some reason. import { query } from 'jsonpath' does not work
 

package/src/OntologyManager/OntologyStore/index.test.ts

@@ -1,3 +1,5 @@
+/* eslint-disable @typescript-eslint/no-unsafe-return */
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 import path from 'node:path'
 
 import { beforeAll, describe, expect, it, jest } from '@jest/globals'
@@ -17,7 +19,7 @@ const prefixes = new Map([
 // different "Object". This intercepts calls to "query" in this test and makes
 // sure the main scope "Object" is used.
 jest.mock('jsonpath', () => {
-  const original = jest.requireActual('jsonpath') as typeof import('jsonpath')
+  const original = jest.requireActual<typeof import('jsonpath')>('jsonpath')
   return {
     ...original,
     // eslint-disable-next-line @typescript-eslint/no-explicit-any

package/src/OntologyManager/OntologyStore/index.ts

@@ -1,3 +1,5 @@
+/* eslint-disable @typescript-eslint/no-throw-literal */
+/* eslint-disable unicorn/no-await-expression-member */
 import {
   BlobLocation,
   LocalPathLocation,
@@ -193,7 +195,7 @@ export default class OntologyStore {
     return myTx.objectStore('nodes').count()
   }
 
-  private async unique<ITEM extends { id: string }>(nodes: ITEM[]) {
+  private unique<ITEM extends { id: string }>(nodes: ITEM[]) {
     const seen = new Map<string, boolean>()
     const result: ITEM[] = []
     for (const node of nodes) {
@@ -303,10 +305,7 @@ export default class OntologyStore {
       await Promise.all(
         [...queryIds].map(async (queryId) => {
           const theseResults = (
-            (await myTx
-              .objectStore('edges')
-              .index(queryIndex)
-              .getAll(queryId)) as OntologyDBEdge[]
+            await myTx.objectStore('edges').index(queryIndex).getAll(queryId)
           )
             .filter((element) => filterEdge(element))
             .map((edge) => edge[resultProp])

package/src/OntologyManager/OntologyStore/indexeddb-storage.ts

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import { openLocation } from '@jbrowse/core/util/io'
 import equal from 'fast-deep-equal/es6'
 import { IDBPDatabase, IDBPTransaction, openDB } from 'idb/with-async-ittr'
@@ -174,7 +175,7 @@ export async function isDatabaseCurrent(this: OntologyStore, db: Database) {
   }
   // check that the index paths and prefixes are the same as our current ones
   return (
-    equal(this.options.prefixes, meta.storeOptions?.prefixes) &&
-    equal(this.options.textIndexing, meta.storeOptions?.textIndexing)
+    equal(this.options.prefixes, meta.storeOptions.prefixes) &&
+    equal(this.options.textIndexing, meta.storeOptions.textIndexing)
   )
 }

package/src/SixFrameFeatureDisplay/stateModel.ts

@@ -1,3 +1,9 @@
+/* eslint-disable @typescript-eslint/no-unsafe-return */
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
+/* eslint-disable @typescript-eslint/no-unsafe-member-access */
+/* eslint-disable @typescript-eslint/no-unsafe-argument */
+/* eslint-disable @typescript-eslint/unbound-method */
 import { AnnotationFeatureI } from '@apollo-annotation/apollo-mst'
 import { ConfigurationReference } from '@jbrowse/core/configuration'
 import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
@@ -141,7 +147,7 @@ export function stateModelFactory(
       },
       get changeManager() {
         const session = getSession(self) as ApolloSession
-        return session.apolloDataStore?.changeManager
+        return session.apolloDataStore.changeManager
       },
       get sequence() {
         const { regions } = self
@@ -348,7 +354,7 @@ export function stateModelFactory(
     .actions((self) => ({
       setSelectedFeature(feature?: AnnotationFeatureI) {
         const session = getSession(self) as ApolloSession
-        return session.apolloSetSelectedFeature(feature)
+        session.apolloSetSelectedFeature(feature)
       },
       setApolloFeatureUnderMouse(feature?: AnnotationFeatureI) {
         self.apolloFeatureUnderMouse = feature
@@ -388,19 +394,25 @@ export function stateModelFactory(
             label: 'Show start codons',
             type: 'checkbox',
             checked: self.showStartCodons,
-            onClick: () => self.toggleShowStartCodons(),
+            onClick: () => {
+              self.toggleShowStartCodons()
+            },
           },
           {
             label: 'Show stop codons',
             type: 'checkbox',
             checked: self.showStopCodons,
-            onClick: () => self.toggleShowStopCodons(),
+            onClick: () => {
+              self.toggleShowStopCodons()
+            },
           },
           {
             label: 'Show intron lines',
             type: 'checkbox',
             checked: self.showIntronLines,
-            onClick: () => self.toggleShowIntronLines(),
+            onClick: () => {
+              self.toggleShowIntronLines()
+            },
           },
         ]
       },

package/src/TabularEditor/HybridGrid/Feature.tsx

@@ -1,3 +1,7 @@
+/* eslint-disable @typescript-eslint/unbound-method */
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
+/* eslint-disable @typescript-eslint/no-unsafe-member-access */
+/* eslint-disable @typescript-eslint/no-unsafe-argument */
 import { AnnotationFeatureI } from '@apollo-annotation/apollo-mst'
 import { AbstractSessionModel } from '@jbrowse/core/util'
 import { observer } from 'mobx-react'
@@ -127,8 +131,9 @@ export const Feature = observer(function Feature({
   }
 
   // pop up a snackbar in the session notifying user of an error
-  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')
+  }
 
   return (
     <>

package/src/TabularEditor/HybridGrid/FeatureAttributes.tsx

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/restrict-template-expressions */
 import { AnnotationFeatureI } from '@apollo-annotation/apollo-mst'
 import { observer } from 'mobx-react'
 import { getSnapshot } from 'mobx-state-tree'

package/src/TabularEditor/HybridGrid/HybridGrid.tsx

@@ -48,9 +48,9 @@ const HybridGrid = observer(function HybridGrid({
   useEffect(() => {
     const scrollContainer = scrollContainerRef.current
     if (scrollContainer && selectedFeature) {
-      const selectedRow = scrollContainer.querySelector(
+      const selectedRow = scrollContainer.querySelector<HTMLTableRowElement>(
         `.${classes.selectedFeature}`,
-      ) as HTMLElement | null
+      )
       if (selectedRow) {
         const currScroll = scrollContainer.scrollTop
         const newScrollTop = selectedRow.offsetTop - 25

package/src/TabularEditor/HybridGrid/NumberCell.tsx

@@ -70,7 +70,9 @@ export const NumberCell = observer(function NumberCell({
             onChangeCommitted(value).catch(notifyError)
           }
         }}
-        ref={(node) => setInputNode(node)}
+        ref={(node) => {
+          setInputNode(node)
+        }}
       />
     </span>
   )

package/src/TabularEditor/HybridGrid/ToolBar.tsx

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/unbound-method */
 import ClearIcon from '@mui/icons-material/Clear'
 import UnfoldLessIcon from '@mui/icons-material/UnfoldLess'
 import { IconButton, InputAdornment, TextField, Tooltip } from '@mui/material'
@@ -43,11 +44,17 @@ export const ToolBar = observer(function ToolBar({
         value={model.filterText}
         sx={{ marginTop: 0 }}
         variant="outlined"
-        onChange={(event) => model.setFilterText(event.target.value)}
+        onChange={(event) => {
+          model.setFilterText(event.target.value)
+        }}
         InputProps={{
           endAdornment: (
             <InputAdornment position="end">
-              <IconButton onClick={() => model.clearFilterText()}>
+              <IconButton
+                onClick={() => {
+                  model.clearFilterText()
+                }}
+              >
                 <ClearIcon />
               </IconButton>
             </InputAdornment>

package/src/components/AddAssembly.tsx

@@ -1,3 +1,9 @@
+/* eslint-disable @typescript-eslint/no-unsafe-enum-comparison */
+/* eslint-disable @typescript-eslint/unbound-method */
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
+/* eslint-disable @typescript-eslint/no-unsafe-member-access */
+/* eslint-disable @typescript-eslint/no-misused-promises */
 import {
   AddAssemblyAndFeaturesFromFileChange,
   AddAssemblyFromExternalChange,
@@ -78,7 +84,7 @@ export function AddAssembly({
   const [fastaGziIndexFile, setFastaGziIndexFile] = useState('')
   const [loading, setLoading] = useState(false)
 
-  function handleChangeInternetAccount(e: SelectChangeEvent<string>) {
+  function handleChangeInternetAccount(e: SelectChangeEvent) {
     setSubmitted(false)
     const newlySelectedInternetAccount = apolloInternetAccounts.find(
       (ia) => ia.internetAccountId === e.target.value,
@@ -350,9 +356,9 @@ export function AddAssembly({
                 fullWidth
                 variant="outlined"
                 error={!validFastaFile}
-                onChange={(e: React.ChangeEvent<HTMLInputElement>) =>
+                onChange={(e: React.ChangeEvent<HTMLInputElement>) => {
                   setFastaFile(e.target.value)
-                }
+                }}
                 disabled={submitted && !errorMessage}
                 InputProps={{
                   startAdornment: (
@@ -371,9 +377,9 @@ export function AddAssembly({
                 fullWidth
                 variant="outlined"
                 error={!validFastaIndexFile}
-                onChange={(e: React.ChangeEvent<HTMLInputElement>) =>
+                onChange={(e: React.ChangeEvent<HTMLInputElement>) => {
                   setFastaIndexFile(e.target.value)
-                }
+                }}
                 disabled={submitted && !errorMessage}
                 InputProps={{
                   startAdornment: (
@@ -392,9 +398,9 @@ export function AddAssembly({
                 fullWidth
                 variant="outlined"
                 error={Boolean(fastaGziIndexFile) && !validFastaGziIndexFile}
-                onChange={(e: React.ChangeEvent<HTMLInputElement>) =>
+                onChange={(e: React.ChangeEvent<HTMLInputElement>) => {
                   setFastaGziIndexFile(e.target.value)
-                }
+                }}
                 disabled={submitted && !errorMessage}
                 InputProps={{
                   startAdornment: (
@@ -417,7 +423,9 @@ export function AddAssembly({
                   control={
                     <Checkbox
                       checked={fileType === FileType.GFF3 && importFeatures}
-                      onChange={() => setImportFeatures(!importFeatures)}
+                      onChange={() => {
+                        setImportFeatures(!importFeatures)
+                      }}
                       disabled={
                         fileType !== FileType.GFF3 ||
                         (submitted && !errorMessage)

package/src/components/AddChildFeature.tsx

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/no-misused-promises */
 import { AnnotationFeatureI } from '@apollo-annotation/apollo-mst'
 import { AddFeatureChange } from '@apollo-annotation/apollo-shared'
 import { AbstractSessionModel } from '@jbrowse/core/util'
@@ -96,7 +97,7 @@ export function AddChildFeature({
       },
       parentFeatureId: sourceFeature._id,
     })
-    await changeManager.submit?.(change)
+    await changeManager.submit(change)
     notify('Feature added successfully', 'success')
     handleClose()
     event.preventDefault()
@@ -111,7 +112,7 @@ export function AddChildFeature({
       setShowPhase(false)
     }
   }
-  async function handleChangePhase(e: SelectChangeEvent<string>) {
+  function handleChangePhase(e: SelectChangeEvent) {
     setErrorMessage('')
     setPhase(e.target.value)
 
@@ -153,7 +154,9 @@ export function AddChildFeature({
             fullWidth
             variant="outlined"
             value={start}
-            onChange={(e) => setStart(e.target.value)}
+            onChange={(e) => {
+              setStart(e.target.value)
+            }}
           />
           <TextField
             margin="dense"
@@ -163,7 +166,9 @@ export function AddChildFeature({
             fullWidth
             variant="outlined"
             value={end}
-            onChange={(e) => setEnd(e.target.value)}
+            onChange={(e) => {
+              setEnd(e.target.value)
+            }}
             error={error}
             helperText={error ? '"End" must be greater than "Start"' : null}
           />

package/src/components/AddFeature.tsx

@@ -1,3 +1,5 @@
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
+/* eslint-disable @typescript-eslint/no-misused-promises */
 import { AddFeatureChange } from '@apollo-annotation/apollo-shared'
 import { AbstractSessionModel, Region } from '@jbrowse/core/util/types'
 import {
@@ -90,7 +92,7 @@ export function AddFeature({
         strand,
       },
     })
-    await changeManager.submit?.(change)
+    await changeManager.submit(change)
     notify('Feature added successfully', 'success')
     handleClose()
     event.preventDefault()
@@ -107,7 +109,7 @@ export function AddFeature({
     }
   }
 
-  function handleChangeStrand(e: SelectChangeEvent<string>) {
+  function handleChangeStrand(e: SelectChangeEvent) {
     setErrorMessage('')
 
     switch (Number(e.target.value)) {
@@ -126,7 +128,7 @@ export function AddFeature({
     }
   }
 
-  async function handleChangePhase(e: SelectChangeEvent<string>) {
+  function handleChangePhase(e: SelectChangeEvent) {
     setErrorMessage('')
     setPhase(e.target.value)
 
@@ -170,7 +172,9 @@ export function AddFeature({
             fullWidth
             variant="outlined"
             value={Number(start)}
-            onChange={(e) => setStart(e.target.value)}
+            onChange={(e) => {
+              setStart(e.target.value)
+            }}
           />
           <TextField
             margin="dense"
@@ -180,7 +184,9 @@ export function AddFeature({
             fullWidth
             variant="outlined"
             value={end}
-            onChange={(e) => setEnd(e.target.value)}
+            onChange={(e) => {
+              setEnd(e.target.value)
+            }}
             error={error}
             helperText={error ? '"End" must be greater than "Start"' : null}
           />

package/src/components/CopyFeature.tsx

@@ -1,3 +1,6 @@
+/* eslint-disable @typescript-eslint/no-unsafe-argument */
+/* eslint-disable @typescript-eslint/no-misused-promises */
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 import {
   AnnotationFeatureI,
   AnnotationFeatureSnapshot,
@@ -88,7 +91,7 @@ export function CopyFeature({
   const [start, setStart] = useState(sourceFeature.start)
   const [errorMessage, setErrorMessage] = useState('')
 
-  async function handleChangeAssembly(e: SelectChangeEvent<string>) {
+  function handleChangeAssembly(e: SelectChangeEvent) {
     setSelectedAssemblyId(e.target.value)
   }
 
@@ -113,11 +116,13 @@ export function CopyFeature({
       setRefNames(newRefNames)
       setSelectedRefSeqId(newRefNames[0]?._id || '')
     }
-    getRefNames().catch((error) => setErrorMessage(String(error)))
+    getRefNames().catch((error) => {
+      setErrorMessage(String(error))
+    })
   }, [selectedAssemblyId, assemblyManager])
 
-  async function handleChangeRefSeq(e: SelectChangeEvent<string>) {
-    const refSeq = e.target.value as string
+  function handleChangeRefSeq(e: SelectChangeEvent) {
+    const refSeq = e.target.value
     setSelectedRefSeqId(refSeq)
   }
 
@@ -133,7 +138,7 @@ export function CopyFeature({
       setErrorMessage(`Assembly not found: ${selectedAssemblyId}.`)
       return
     }
-    const canonicalRefName = assembly?.getCanonicalRefName(selectedRefSeqId)
+    const canonicalRefName = assembly.getCanonicalRefName(selectedRefSeqId)
     const region = assembly.regions?.find((r) => r.refName === canonicalRefName)
     if (!region) {
       setErrorMessage(`RefSeq not found: ${selectedRefSeqId}.`)
@@ -208,7 +213,7 @@ export function CopyFeature({
       copyFeature: true,
       allIds: featureIds,
     })
-    await changeManager.submit?.(change)
+    await changeManager.submit(change)
 
     notify('Feature copied successfully', 'success')
     handleClose()

package/src/components/DeleteAssembly.tsx

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/no-misused-promises */
 import { DeleteAssemblyChange } from '@apollo-annotation/apollo-shared'
 import { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import {
@@ -67,7 +68,7 @@ export function DeleteAssembly({
     }
   }, [assemblies, selectedAssembly])
 
-  function handleChangeInternetAccount(e: SelectChangeEvent<string>) {
+  function handleChangeInternetAccount(e: SelectChangeEvent) {
     setSubmitted(false)
     const newlySelectedInternetAccount = apolloInternetAccounts.find(
       (ia) => ia.internetAccountId === e.target.value,
@@ -80,7 +81,7 @@ export function DeleteAssembly({
     setSelectedInternetAccount(newlySelectedInternetAccount)
   }
 
-  function handleChangeAssembly(e: SelectChangeEvent<string>) {
+  function handleChangeAssembly(e: SelectChangeEvent) {
     const newAssembly = assemblies.find((asm) => asm.name === e.target.value)
     setSelectedAssembly(newAssembly)
   }
@@ -97,7 +98,7 @@ export function DeleteAssembly({
       typeName: 'DeleteAssemblyChange',
       assembly: selectedAssembly.name,
     })
-    await changeManager.submit?.(change, {
+    await changeManager.submit(change, {
       internetAccountId: selectedInternetAccount.internetAccountId,
     })
     handleClose()
@@ -154,7 +155,9 @@ export function DeleteAssembly({
               control={
                 <Checkbox
                   checked={confirmDelete}
-                  onChange={() => setconfirmDelete(!confirmDelete)}
+                  onChange={() => {
+                    setconfirmDelete(!confirmDelete)
+                  }}
                 />
               }
               label="I understand that all assembly data will be deleted"

package/src/components/DeleteFeature.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-misused-promises */
 import { AnnotationFeatureI } from '@apollo-annotation/apollo-mst'
 import { DeleteFeatureChange } from '@apollo-annotation/apollo-shared'
 import { AbstractSessionModel } from '@jbrowse/core/util'
@@ -51,7 +54,7 @@ export function DeleteFeature({
       deletedFeature: getSnapshot(sourceFeature),
       parentFeatureId: sourceFeature.parent?._id,
     })
-    await changeManager.submit?.(change)
+    await changeManager.submit(change)
     notify('Feature deleted successfully', 'success')
     handleClose()
     event.preventDefault()

package/src/components/Dialog.tsx

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/unbound-method */
 import { Dialog as JBDialog } from '@jbrowse/core/ui'
 import CloseIcon from '@mui/icons-material/Close'
 import { DialogProps, DialogTitle, IconButton } from '@mui/material'

package/src/components/DownloadGFF3.tsx

@@ -1,3 +1,8 @@
+/* eslint-disable @typescript-eslint/unbound-method */
+/* eslint-disable @typescript-eslint/no-unsafe-argument */
+/* eslint-disable @typescript-eslint/no-unsafe-member-access */
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
+/* eslint-disable @typescript-eslint/no-misused-promises */
 import { ApolloAssembly } from '@apollo-annotation/apollo-mst'
 import { makeGFF3Feature } from '@apollo-annotation/apollo-shared'
 import gff, { GFF3Item } from '@gmod/gff'
@@ -48,7 +53,7 @@ export function DownloadGFF3({ handleClose, session }: DownloadGFF3Props) {
     ...inMemoryFileDriver.getAssemblies(),
   ]
 
-  function handleChangeAssembly(e: SelectChangeEvent<string>) {
+  function handleChangeAssembly(e: SelectChangeEvent) {
     const newAssembly = assemblies.find((asm) => asm.name === e.target.value)
     setSelectedAssembly(newAssembly)
   }
@@ -143,7 +148,7 @@ export function DownloadGFF3({ handleClose, session }: DownloadGFF3Props) {
       })
     }
     for (const [, refSeq] of refSeqs) {
-      const features = refSeq?.features
+      const { features } = refSeq
       if (!features) {
         continue
       }

package/src/components/ImportFeatures.tsx

@@ -1,3 +1,9 @@
+/* eslint-disable @typescript-eslint/unbound-method */
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
+/* eslint-disable @typescript-eslint/no-unsafe-argument */
+/* eslint-disable @typescript-eslint/no-unsafe-member-access */
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
+/* eslint-disable @typescript-eslint/no-misused-promises */
 import { AddFeaturesFromFileChange } from '@apollo-annotation/apollo-shared'
 import { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import { getConf } from '@jbrowse/core/configuration'
@@ -55,7 +61,7 @@ export function ImportFeatures({
   }
   const assemblies = collaborationServerDriver.getAssemblies()
 
-  function handleChangeAssembly(e: SelectChangeEvent<string>) {
+  function handleChangeAssembly(e: SelectChangeEvent) {
     const newAssembly = assemblies.find((asm) => asm.name === e.target.value)
     setSelectedAssembly(newAssembly)
     setSubmitted(false)
@@ -90,7 +96,7 @@ export function ImportFeatures({
         assemblyId: selectedAssembly.name,
       })
       uri.search = searchParams.toString()
-      const fetch = apolloInternetAccount?.getFetcher({
+      const fetch = apolloInternetAccount.getFetcher({
         locationType: 'UriLocation',
         uri: uri.toString(),
       })
@@ -157,7 +163,7 @@ export function ImportFeatures({
     formData.append('file', file)
     formData.append('fileName', file.name)
     formData.append('type', 'text/x-gff3')
-    const apolloFetchFile = apolloInternetAccount?.getFetcher({
+    const apolloFetchFile = apolloInternetAccount.getFetcher({
       locationType: 'UriLocation',
       uri: url,
     })

package/src/components/ManageChecks.tsx

@@ -1,3 +1,5 @@
+/* eslint-disable @typescript-eslint/unbound-method */
+/* eslint-disable @typescript-eslint/no-misused-promises */
 import { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import { AbstractSessionModel } from '@jbrowse/core/util'
 import {
@@ -90,7 +92,9 @@ export function ManageChecks({ handleClose, session }: ManageChecksProps) {
       const data = (await response.json()) as CheckDocument[]
       setChecks(data)
     }
-    getChecks().catch((error) => setErrorMessage(String(error)))
+    getChecks().catch((error) => {
+      setErrorMessage(String(error))
+    })
   }, [selectedInternetAccount])
 
   useEffect(() => {
@@ -119,10 +123,12 @@ export function ManageChecks({ handleClose, session }: ManageChecksProps) {
       const assembly = (await response.json()) as AssemblyDocument
       setSelectedChecks(assembly.checks)
     }
-    getChecks().catch((error) => setErrorMessage(String(error)))
+    getChecks().catch((error) => {
+      setErrorMessage(String(error))
+    })
   }, [selectedAssembly, selectedInternetAccount])
 
-  function handleChangeAssembly(e: SelectChangeEvent<string>) {
+  function handleChangeAssembly(e: SelectChangeEvent) {
     const newAssembly = assemblies.find((asm) => asm.name === e.target.value)
     setSelectedAssembly(newAssembly)
   }
@@ -182,7 +188,7 @@ export function ManageChecks({ handleClose, session }: ManageChecksProps) {
     }
   }
 
-  function handleChangeInternetAccount(e: SelectChangeEvent<string>) {
+  function handleChangeInternetAccount(e: SelectChangeEvent) {
     setSubmitted(false)
     const newlySelectedInternetAccount = apolloInternetAccounts.find(
       (ia) => ia.internetAccountId === e.target.value,