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

package/src/components/ManageUsers.tsx

@@ -1,3 +1,8 @@
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
+/* eslint-disable @typescript-eslint/no-misused-promises */
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
+/* eslint-disable @typescript-eslint/no-unsafe-member-access */
+/* eslint-disable @typescript-eslint/no-unsafe-return */
 import { DeleteUserChange, UserChange } from '@apollo-annotation/apollo-shared'
 import { AbstractRootModel } from '@jbrowse/core/util'
 import DeleteIcon from '@mui/icons-material/Delete'
@@ -67,7 +72,7 @@ export function ManageUsers({
   const getUsers = useCallback(async () => {
     const { baseURL } = selectedInternetAccount
     const uri = new URL('/users', baseURL).href
-    const apolloFetch = selectedInternetAccount?.getFetcher({
+    const apolloFetch = selectedInternetAccount.getFetcher({
       locationType: 'UriLocation',
       uri,
     })
@@ -87,7 +92,9 @@ export function ManageUsers({
   }, [selectedInternetAccount])
 
   useEffect(() => {
-    getUsers().catch((error) => setErrorMessage(String(error)))
+    getUsers().catch((error) => {
+      setErrorMessage(String(error))
+    })
   }, [getUsers])
 
   async function deleteUser(id: GridRowId) {
@@ -138,7 +145,7 @@ export function ManageUsers({
     },
   ]
 
-  function handleChangeInternetAccount(e: SelectChangeEvent<string>) {
+  function handleChangeInternetAccount(e: SelectChangeEvent) {
     const newlySelectedInternetAccount = apolloInternetAccounts.find(
       (ia) => ia.internetAccountId === e.target.value,
     )
@@ -199,7 +206,9 @@ export function ManageUsers({
               !isCurrentUser(params.id)
             }
             processRowUpdate={processRowUpdate}
-            onProcessRowUpdateError={(error) => setErrorMessage(String(error))}
+            onProcessRowUpdateError={(error) => {
+              setErrorMessage(String(error))
+            }}
           />
         </div>
       </DialogContent>

package/src/components/ModifyFeatureAttribute.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'
@@ -219,7 +222,7 @@ export function ModifyFeatureAttribute({
       featureId: sourceFeature._id,
       attributes: attrs,
     })
-    await changeManager.submit?.(change)
+    await changeManager.submit(change)
     notify('Feature attributes modified successfully', 'success')
     handleClose()
     event.preventDefault()

package/src/components/OntologyTermAutocomplete.tsx

@@ -1,3 +1,7 @@
+/* eslint-disable @typescript-eslint/no-unused-vars */
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
+/* eslint-disable @typescript-eslint/no-unsafe-argument */
+/* eslint-disable @typescript-eslint/no-unsafe-member-access */
 import { AbstractSessionModel, isAbortException } from '@jbrowse/core/util'
 import {
   Autocomplete,
@@ -54,8 +58,7 @@ export function OntologyTermAutocomplete({
     OntologyTerm | undefined
   >()
 
-  const ontologyManager = session.apolloDataStore
-    .ontologyManager as OntologyManager
+  const { ontologyManager } = session.apolloDataStore
   const ontologyStore = ontologyManager.findOntology(
     ontologyName,
     ontologyVersion,
@@ -136,8 +139,8 @@ export function OntologyTermAutocomplete({
     fetchValidTerms,
   ])
 
-  const handleChange = async (
-    event: React.SyntheticEvent<Element, Event>,
+  const handleChange = (
+    event: React.SyntheticEvent,
     newValue?: OntologyTerm | string | null,
   ) => {
     if (!newValue) {

package/src/components/OntologyTermMultiSelect.tsx

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import { isAbortException } from '@jbrowse/core/util'
 import {
   Autocomplete,
@@ -120,8 +121,7 @@ export function OntologyTermMultiSelect({
   includeDeprecated?: boolean
   onChange(newValue: string[]): void
 }) {
-  const ontologyManager = session.apolloDataStore
-    .ontologyManager as OntologyManager
+  const { ontologyManager } = session.apolloDataStore
   const ontology = ontologyManager.findOntology(ontologyName, ontologyVersion)
 
   const [value, setValue] = React.useState<TermValue[]>(

package/src/components/OpenLocalFile.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 { AbstractSessionModel, isElectron } from '@jbrowse/core/util'
 import {
   Button,
@@ -43,7 +46,7 @@ export function OpenLocalFile({ handleClose, session }: OpenLocalFileProps) {
   const [submitted, setSubmitted] = useState(false)
   const theme = useTheme()
 
-  async function handleChangeFile(e: React.ChangeEvent<HTMLInputElement>) {
+  function handleChangeFile(e: React.ChangeEvent<HTMLInputElement>) {
     const selectedFile = e.target.files?.item(0)
     if (!selectedFile) {
       return
@@ -103,9 +106,9 @@ export function OpenLocalFile({ handleClose, session }: OpenLocalFileProps) {
     if (a) {
       // @ts-expect-error MST type coercion problem?
       addApolloTrackConfig(a)
-      notify(`Loaded GFF3 ${file?.name}`, 'success')
+      notify(`Loaded GFF3 ${file.name}`, 'success')
     } else {
-      notify(`Error loading GFF3 ${file?.name}`, 'error')
+      notify(`Error loading GFF3 ${file.name}`, 'error')
     }
     handleClose()
   }

package/src/components/ViewChangeLog.tsx

@@ -1,3 +1,8 @@
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
+/* 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-return */
 import { changeRegistry } from '@apollo-annotation/apollo-common'
 import {
   Button,
@@ -115,7 +120,9 @@ export function ViewChangeLog({ handleClose, session }: ViewChangeLogProps) {
         setAssemblyCollection(data)
       }
     }
-    getAssemblies().catch((error) => setErrorMessage(String(error)))
+    getAssemblies().catch((error) => {
+      setErrorMessage(String(error))
+    })
   }, [apolloInternetAccount, baseURL])
 
   useEffect(() => {
@@ -155,11 +162,13 @@ export function ViewChangeLog({ handleClose, session }: ViewChangeLogProps) {
         setDisplayGridData(data)
       }
     }
-    getGridData().catch((error) => setErrorMessage(String(error)))
+    getGridData().catch((error) => {
+      setErrorMessage(String(error))
+    })
   }, [assemblyId, apolloInternetAccount, baseURL])
 
-  async function handleChangeAssembly(e: SelectChangeEvent<string>) {
-    setAssemblyId(e.target.value as string)
+  function handleChangeAssembly(e: SelectChangeEvent) {
+    setAssemblyId(e.target.value)
   }
 
   return (

package/src/components/ViewCheckResults.tsx

@@ -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-return */
 import { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import {
   Button,
@@ -94,10 +98,12 @@ export function ViewCheckResults({
         setDisplayGridData(data)
       }
     }
-    getGridData().catch((error) => setErrorMessage(String(error)))
+    getGridData().catch((error) => {
+      setErrorMessage(String(error))
+    })
   }, [selectedAssembly, apolloInternetAccount, baseURL])
 
-  function handleChangeAssembly(e: SelectChangeEvent<string>) {
+  function handleChangeAssembly(e: SelectChangeEvent) {
     const newAssembly = assemblies.find((asm) => asm.name === e.target.value)
     setSelectedAssembly(newAssembly)
   }

package/src/extensions/annotationFromPileup.ts

@@ -1,3 +1,8 @@
+/* eslint-disable @typescript-eslint/no-unsafe-argument */
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
+/* eslint-disable @typescript-eslint/no-unsafe-member-access */
+/* eslint-disable @typescript-eslint/no-unsafe-call */
+/* eslint-disable @typescript-eslint/no-unsafe-return */
 import { AnnotationFeatureSnapshot } from '@apollo-annotation/apollo-mst'
 import { AddFeatureChange } from '@apollo-annotation/apollo-shared'
 import { Assembly } from '@jbrowse/core/assemblyManager/assembly'
@@ -150,7 +155,7 @@ export function annotationFromPileup(pluggableElement: PluggableElementBase) {
           cdsFeature.start = Math.min(cdsFeature.start, exon.start)
           cdsFeature.end = Math.max(cdsFeature.end, exon.end)
           const { end, start } = exon
-          discontinuousLocations?.push({ start, end, phase })
+          discontinuousLocations.push({ start, end, phase })
           const localPhase = (end - start) % 3
           phase = ((phase + localPhase) % 3) as 0 | 1 | 2
           const newExon: AnnotationFeatureSnapshot = {
@@ -180,7 +185,7 @@ export function annotationFromPileup(pluggableElement: PluggableElementBase) {
         const session = getSession(self)
         await (
           session as unknown as ApolloSessionModel
-        ).apolloDataStore.changeManager.submit?.(change)
+        ).apolloDataStore.changeManager.submit(change)
         session.notify('Annotation added successfully', 'success')
       },
     }))

package/src/index.ts

@@ -1,3 +1,7 @@
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
+/* eslint-disable @typescript-eslint/unbound-method */
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
+/* eslint-disable @typescript-eslint/no-misused-promises */
 import { changeRegistry, checkRegistry } from '@apollo-annotation/apollo-common'
 import {
   CDSCheck,

package/src/makeDisplayComponent.tsx

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/unbound-method */
 import PluginManager from '@jbrowse/core/PluginManager'
 import type LinearGenomeViewPlugin from '@jbrowse/plugin-linear-genome-view'
 import ExpandLessIcon from '@mui/icons-material/ExpandLess'
@@ -173,10 +174,9 @@ export const DisplayComponent = observer(function DisplayComponent({
   }
 
   const canvasScrollContainerRef = useRef<HTMLDivElement>(null)
-  useEffect(
-    () => scrollSelectedFeatureIntoView(model, canvasScrollContainerRef),
-    [model, selectedFeature],
-  )
+  useEffect(() => {
+    scrollSelectedFeatureIntoView(model, canvasScrollContainerRef)
+  }, [model, selectedFeature])
   return (
     <div className={classes.details} style={{ height: overallHeight }}>
       <AccordionControl

package/src/session/ClientDataStore.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-call */
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
+/* eslint-disable @typescript-eslint/no-unsafe-argument */
 import { ClientDataStore as ClientDataStoreType } from '@apollo-annotation/apollo-common'
 import {
   AnnotationFeature,

package/src/session/session.ts

@@ -1,3 +1,7 @@
+/* eslint-disable @typescript-eslint/no-unused-vars */
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
+/* eslint-disable @typescript-eslint/no-unsafe-argument */
 import { ClientDataStore as ClientDataStoreType } from '@apollo-annotation/apollo-common'
 import {
   AnnotationFeature,
@@ -158,10 +162,7 @@ export function extendSession(
           }
         }
         if (locations.length === 0) {
-          for (const internetAccount of internetAccounts as (
-            | BaseInternetAccountModel
-            | ApolloInternetAccountModel
-          )[]) {
+          for (const internetAccount of internetAccounts) {
             if ('baseURL' in internetAccount) {
               internetAccount.postUserLocation([])
             }
@@ -170,10 +171,7 @@ export function extendSession(
         }
 
         const allLocations: UserLocation[] = []
-        for (const internetAccount of internetAccounts as (
-          | BaseInternetAccountModel
-          | ApolloInternetAccountModel
-        )[]) {
+        for (const internetAccount of internetAccounts) {
           if ('baseURL' in internetAccount) {
             for (const location of locations) {
               const tmpLoc: UserLocation = {
@@ -208,7 +206,7 @@ export function extendSession(
               }
               const lgv = view as unknown as LinearGenomeViewModel
               if (lgv.initialized) {
-                const { dynamicBlocks } = lgv as LinearGenomeViewModel
+                const { dynamicBlocks } = lgv
                 // eslint-disable-next-line unicorn/no-array-for-each
                 dynamicBlocks.forEach((block) => {
                   if (block.regionNumber !== undefined) {
@@ -219,10 +217,7 @@ export function extendSession(
               }
             }
             if (locations.length === 0) {
-              for (const internetAccount of internetAccounts as (
-                | BaseInternetAccountModel
-                | ApolloInternetAccountModel
-              )[]) {
+              for (const internetAccount of internetAccounts) {
                 if ('baseURL' in internetAccount) {
                   internetAccount.postUserLocation([])
                 }
@@ -231,10 +226,7 @@ export function extendSession(
             }
 
             const allLocations: UserLocation[] = []
-            for (const internetAccount of internetAccounts as (
-              | BaseInternetAccountModel
-              | ApolloInternetAccountModel
-            )[]) {
+            for (const internetAccount of internetAccounts) {
               if ('baseURL' in internetAccount) {
                 for (const location of locations) {
                   const tmpLoc: UserLocation = {

package/src/util/loadAssemblyIntoClient.ts

@@ -82,7 +82,8 @@ export async function checkFeatures(
       for (const check of checkRegistry.getChecks().values()) {
         const result: CheckResultSnapshot[] = await check.checkFeature(
           getSnapshot(feature),
-          async (start: number, stop: number) => ref.getSequence(start, stop),
+          (start: number, stop: number) =>
+            Promise.resolve(ref.getSequence(start, stop)),
         )
         checkResults.push(...result)
       }
@@ -202,14 +203,14 @@ function createFeature(gff3Feature: GFF3Feature): AnnotationFeatureSnapshot {
     }
   }
 
-  if (childFeatures?.length) {
+  if (childFeatures.length > 0) {
     const children: Record<string, AnnotationFeatureSnapshot> = {}
     for (const childFeature of childFeatures) {
       const child = createFeature(childFeature)
       children[child._id] = child
       // Add value to gffId
       child.attributes?._id
-        ? (child.gffId = child.attributes?._id.toString())
+        ? (child.gffId = child.attributes._id.toString())
         : (child.gffId = child._id)
     }
     feature.children = children