@apollo-annotation/jbrowse-plugin-apollo 0.1.21 → 0.2.0

package/src/LinearApolloDisplay/glyphs/GeneGlyph.ts

@@ -13,35 +13,49 @@ import { Glyph } from './Glyph'
 import { boxGlyph } from './BoxGlyph'
 import { LinearApolloDisplayRendering } from '../stateModel/rendering'
 
-let forwardFill: CanvasPattern | null = null
-let backwardFill: CanvasPattern | null = null
-if ('document' in window) {
+let forwardFillLight: CanvasPattern | null = null
+let backwardFillLight: CanvasPattern | null = null
+let forwardFillDark: CanvasPattern | null = null
+let backwardFillDark: CanvasPattern | null = null
+if ('document' in globalThis) {
   for (const direction of ['forward', 'backward']) {
-    const canvas = document.createElement('canvas')
-    const canvasSize = 10
-    canvas.width = canvas.height = canvasSize
-    const ctx = canvas.getContext('2d')
-    if (ctx) {
-      const stripeColor1 = 'rgba(0,0,0,0)'
-      const stripeColor2 = 'rgba(255,255,255,0.25)'
-      const gradient =
-        direction === 'forward'
-          ? ctx.createLinearGradient(0, canvasSize, canvasSize, 0)
-          : ctx.createLinearGradient(0, 0, canvasSize, canvasSize)
-      gradient.addColorStop(0, stripeColor1)
-      gradient.addColorStop(0.25, stripeColor1)
-      gradient.addColorStop(0.25, stripeColor2)
-      gradient.addColorStop(0.5, stripeColor2)
-      gradient.addColorStop(0.5, stripeColor1)
-      gradient.addColorStop(0.75, stripeColor1)
-      gradient.addColorStop(0.75, stripeColor2)
-      gradient.addColorStop(1, stripeColor2)
-      ctx.fillStyle = gradient
-      ctx.fillRect(0, 0, 10, 10)
-      if (direction === 'forward') {
-        forwardFill = ctx.createPattern(canvas, 'repeat')
-      } else {
-        backwardFill = ctx.createPattern(canvas, 'repeat')
+    for (const themeMode of ['light', 'dark']) {
+      const canvas = document.createElement('canvas')
+      const canvasSize = 10
+      canvas.width = canvas.height = canvasSize
+      const ctx = canvas.getContext('2d')
+      if (ctx) {
+        const stripeColor1 =
+          themeMode === 'light' ? 'rgba(0,0,0,0)' : 'rgba(0,0,0,0.75)'
+        const stripeColor2 =
+          themeMode === 'light' ? 'rgba(255,255,255,0.25)' : 'rgba(0,0,0,0.50)'
+        const gradient =
+          direction === 'forward'
+            ? ctx.createLinearGradient(0, canvasSize, canvasSize, 0)
+            : ctx.createLinearGradient(0, 0, canvasSize, canvasSize)
+        gradient.addColorStop(0, stripeColor1)
+        gradient.addColorStop(0.25, stripeColor1)
+        gradient.addColorStop(0.25, stripeColor2)
+        gradient.addColorStop(0.5, stripeColor2)
+        gradient.addColorStop(0.5, stripeColor1)
+        gradient.addColorStop(0.75, stripeColor1)
+        gradient.addColorStop(0.75, stripeColor2)
+        gradient.addColorStop(1, stripeColor2)
+        ctx.fillStyle = gradient
+        ctx.fillRect(0, 0, 10, 10)
+        if (direction === 'forward') {
+          if (themeMode === 'light') {
+            forwardFillLight = ctx.createPattern(canvas, 'repeat')
+          } else {
+            forwardFillDark = ctx.createPattern(canvas, 'repeat')
+          }
+        } else {
+          if (themeMode === 'light') {
+            backwardFillLight = ctx.createPattern(canvas, 'repeat')
+          } else {
+            backwardFillDark = ctx.createPattern(canvas, 'repeat')
+          }
+        }
       }
     }
   }
@@ -61,13 +75,34 @@ function draw(
   const rowHeight = apolloRowHeight
   const exonHeight = Math.round(0.6 * rowHeight)
   const cdsHeight = Math.round(0.9 * rowHeight)
-  const { strand } = feature
-  const { children } = feature
+  const { children, min, strand } = feature
   if (!children) {
     return
   }
   const { apolloSelectedFeature } = session
 
+  // Draw background for gene
+  const topLevelFeatureMinX =
+    (lgv.bpToPx({
+      refName,
+      coord: min,
+      regionNumber: displayedRegionIndex,
+    })?.offsetPx ?? 0) - offsetPx
+  const topLevelFeatureWidthPx = feature.length / bpPerPx
+  const topLevelFeatureStartPx = reversed
+    ? topLevelFeatureMinX - topLevelFeatureWidthPx
+    : topLevelFeatureMinX
+  const topLevelFeatureTop = row * rowHeight
+  const topLevelFeatureHeight = getRowCount(feature) * rowHeight
+
+  ctx.fillStyle = alpha(theme?.palette.background.paper ?? '#ffffff', 0.6)
+  ctx.fillRect(
+    topLevelFeatureStartPx,
+    topLevelFeatureTop,
+    topLevelFeatureWidthPx,
+    topLevelFeatureHeight,
+  )
+
   // Draw lines on different rows for each mRNA
   let currentRow = 0
   for (const [, mrna] of children) {
@@ -102,6 +137,10 @@ function draw(
     }
   }
 
+  const forwardFill =
+    theme?.palette.mode === 'dark' ? forwardFillDark : forwardFillLight
+  const backwardFill =
+    theme?.palette.mode === 'dark' ? backwardFillDark : backwardFillLight
   // Draw exon and CDS for each mRNA
   currentRow = 0
   for (const [, child] of children) {
@@ -289,11 +328,35 @@ function getFeatureFromLayout(
   bp: number,
   row: number,
 ): AnnotationFeature | undefined {
-  const featureInThisRow: AnnotationFeature[] = featuresForRow(feature)[row]
+  const featureInThisRow: AnnotationFeature[] =
+    featuresForRow(feature)[row] || []
   for (const f of featureInThisRow) {
+    let featureObj
     if (bp >= f.min && bp <= f.max && f.parent) {
-      return f
+      featureObj = f
+    }
+    if (!featureObj) {
+      continue
+    }
+    if (
+      featureObj.type === 'CDS' &&
+      featureObj.parent &&
+      featureObj.parent.type === 'mRNA'
+    ) {
+      const { cdsLocations } = featureObj.parent
+      for (const cdsLoc of cdsLocations) {
+        for (const loc of cdsLoc) {
+          if (bp >= loc.min && bp <= loc.max) {
+            return featureObj
+          }
+        }
+      }
+
+      // If mouse position is in the intron region, return the mRNA
+      return featureObj.parent
     }
+    // If mouse position is in a feature that is not a CDS, return the feature
+    return featureObj
   }
   return feature
 }

package/src/LinearApolloDisplay/stateModel/base.ts

@@ -221,9 +221,11 @@ export function baseModelFactory(
               void (
                 self.session as unknown as ApolloSessionModel
               ).apolloDataStore.loadFeatures(self.regions)
-              void (
-                self.session as unknown as ApolloSessionModel
-              ).apolloDataStore.loadRefSeq(self.regions)
+              if (self.lgv.bpPerPx <= 3) {
+                void (
+                  self.session as unknown as ApolloSessionModel
+                ).apolloDataStore.loadRefSeq(self.regions)
+              }
             },
             { name: 'LinearApolloDisplayLoadFeatures', delay: 1000 },
           ),

package/src/LinearApolloDisplay/stateModel/index.ts

@@ -19,6 +19,6 @@ export function stateModelFactory(
 export type LinearApolloDisplayStateModel = ReturnType<typeof stateModelFactory>
 // eslint disable because of
 // https://mobx-state-tree.js.org/tips/typescript#using-a-mst-type-at-design-time
-// eslint-disable-next-line @typescript-eslint/no-empty-interface
+// eslint-disable-next-line @typescript-eslint/no-empty-object-type
 export interface LinearApolloDisplay
   extends Instance<LinearApolloDisplayStateModel> {}

package/src/LinearApolloDisplay/stateModel/mouseEvents.ts

@@ -499,6 +499,6 @@ export type LinearApolloDisplayMouseEventsModel = ReturnType<
 >
 // eslint disable because of
 // https://mobx-state-tree.js.org/tips/typescript#using-a-mst-type-at-design-time
-// eslint-disable-next-line @typescript-eslint/no-empty-interface
+// eslint-disable-next-line @typescript-eslint/no-empty-object-type
 export interface LinearApolloDisplayMouseEvents
   extends Instance<LinearApolloDisplayMouseEventsModel> {}

package/src/LinearApolloDisplay/stateModel/rendering.ts

@@ -445,6 +445,6 @@ export type LinearApolloDisplayRenderingModel = ReturnType<
 >
 // eslint disable because of
 // https://mobx-state-tree.js.org/tips/typescript#using-a-mst-type-at-design-time
-// eslint-disable-next-line @typescript-eslint/no-empty-interface
+// eslint-disable-next-line @typescript-eslint/no-empty-object-type
 export interface LinearApolloDisplayRendering
   extends Instance<LinearApolloDisplayRenderingModel> {}

package/src/OntologyManager/OntologyStore/fulltext.ts

@@ -2,7 +2,7 @@
 /* eslint-disable @typescript-eslint/no-unsafe-return */
 // jsonpath triggers this rule for some reason. import { query } from 'jsonpath' does not work
 
-import { checkAbortSignal } from '@jbrowse/core/util'
+import { checkAbortSignal } from '@jbrowse/core/util/aborting'
 import jsonpath from 'jsonpath'
 
 import { stopwords } from './fulltext-stopwords'
@@ -170,7 +170,10 @@ export function elaborateMatch(
   const sortedWordIndexes = [...queryWordIndexes].sort()
   const matchedQueryWords = sortedWordIndexes.map((i) => queryWords[i])
   const queryWordRegexps = matchedQueryWords.map((queryWord) => {
-    const escaped = queryWord.replaceAll(/[$()*+./?[\\\]^{|}-]/g, '\\$&')
+    const escaped = queryWord.replaceAll(
+      /[$()*+./?[\\\]^{|}-]/g,
+      String.raw`\$&`,
+    )
     return new RegExp(`\\b${escaped}`, 'gi')
   })
   // const needle = matchedQueryWords.join(' ')

package/src/OntologyManager/OntologyStore/index.ts

@@ -5,9 +5,15 @@ import {
   BlobLocation,
   LocalPathLocation,
   UriLocation,
+  isLocalPathLocation,
   isUriLocation,
 } from '@jbrowse/core/util'
-import { IDBPTransaction, IndexNames, StoreNames } from 'idb/with-async-ittr'
+import {
+  deleteDB,
+  IDBPTransaction,
+  IndexNames,
+  StoreNames,
+} from 'idb/with-async-ittr'
 
 import { textSearch } from './fulltext'
 import { OntologyDB, OntologyDBEdge, isDeprecated } from './indexeddb-schema'
@@ -38,15 +44,6 @@ export type Transaction<
 /** the format of the loading data source */
 type SourceType = 'obo-graph-json' | 'obo' | 'owl'
 
-/**
- * @deprecated use the one from jbrowse core when it is published
- **/
-function isLocalPathLocation(location: unknown): location is LocalPathLocation {
-  return (
-    typeof location === 'object' && location !== null && 'localPath' in location
-  )
-}
-
 async function arrayFromAsync<T>(iter: AsyncIterable<T>) {
   const a = []
   for await (const i of iter) {
@@ -176,18 +173,24 @@ export default class OntologyStore {
       return db
     }
 
-    const { sourceLocation, sourceType } = this
-    if (sourceType === 'obo-graph-json') {
-      await this.loadOboGraphJson(db)
-    } else {
-      throw new Error(
-        `ontology source file ${JSON.stringify(
-          sourceLocation,
-        )} has type ${sourceType}, which is not yet supported`,
-      )
-    }
+    try {
+      const { sourceLocation, sourceType } = this
+      if (sourceType === 'obo-graph-json') {
+        await this.loadOboGraphJson(db)
+      } else {
+        throw new Error(
+          `ontology source file ${JSON.stringify(
+            sourceLocation,
+          )} has type ${sourceType}, which is not yet supported`,
+        )
+      }
 
-    return db
+      return db
+    } catch (error) {
+      db.close()
+      await deleteDB(this.dbName)
+      throw error
+    }
   }
 
   async termCount(tx?: Transaction<['nodes']>) {
@@ -497,7 +500,7 @@ export default class OntologyStore {
 
     // fetch the full nodes and filter out deprecated ones
     const terms: OntologyClass[] = []
-    for await (const termId of termIds) {
+    for (const termId of termIds) {
       const node = await myTx.objectStore('nodes').get(termId)
       if (node && isOntologyClass(node) && !isDeprecated(node)) {
         terms.push(node)

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

@@ -84,9 +84,14 @@ export async function loadOboGraphJson(this: OntologyStore, db: Database) {
   // TODO: using file streaming along with an event-based json parser
   // instead of JSON.parse and .readFile could probably make this faster
   // and less memory intensive
-  const oboGraph = JSON.parse(
-    await openLocation(this.sourceLocation).readFile('utf8'),
-  ) as GraphDocument
+  let oboGraph: GraphDocument
+  try {
+    oboGraph = JSON.parse(
+      await openLocation(this.sourceLocation).readFile('utf8'),
+    ) as GraphDocument
+  } catch {
+    throw new Error('Error in loading ontology')
+  }
 
   const parseTime = Date.now()
 

package/src/OntologyManager/index.ts

@@ -1,15 +1,26 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
+import {
+  AnyConfigurationModel,
+  ConfigurationSchema,
+  readConfObject,
+} from '@jbrowse/core/configuration'
 import {
   BlobLocation,
   LocalPathLocation,
   UriLocation,
 } from '@jbrowse/core/util/types/mst'
 import { autorun } from 'mobx'
-import { Instance, addDisposer, getSnapshot, types } from 'mobx-state-tree'
-
+import {
+  Instance,
+  addDisposer,
+  getRoot,
+  getSnapshot,
+  types,
+} from 'mobx-state-tree'
 import OntologyStore, { OntologyStoreOptions } from './OntologyStore'
 import { OntologyDBNode } from './OntologyStore/indexeddb-schema'
 import { applyPrefixes, expandPrefixes } from './OntologyStore/prefixes'
+import ApolloPluginConfigurationSchema from '../config'
+import { ApolloRootModel } from '../types'
 
 export { isDeprecated } from './OntologyStore/indexeddb-schema'
 
@@ -55,15 +66,27 @@ export const OntologyManagerType = types
       'SO:': 'http://purl.obolibrary.org/obo/SO_',
     }),
   })
+  .views((self) => ({
+    get featureTypeOntologyName(): string {
+      const jbConfig = getRoot<ApolloRootModel>(self).jbrowse
+        .configuration as AnyConfigurationModel
+      const pluginConfiguration = jbConfig.ApolloPlugin as Instance<
+        typeof ApolloPluginConfigurationSchema
+      >
+      const featureTypeOntologyName = readConfObject(
+        pluginConfiguration,
+        'featureTypeOntologyName',
+      ) as string
+      return featureTypeOntologyName
+    },
+  }))
   .views((self) => ({
     /**
      * gets the OntologyRecord for the ontology we should be
      * using for feature types (e.g. SO or maybe biotypes)
      **/
     get featureTypeOntology() {
-      // TODO: change this to read some configuration for which feature type ontology
-      // we should be using. currently hardcoded to use SO.
-      return this.findOntology('Sequence Ontology')
+      return this.findOntology(self.featureTypeOntologyName)
     },
 
     findOntology(name: string, version?: string) {
@@ -157,9 +180,9 @@ export const OntologyRecordConfiguration = ConfigurationSchema(
 
 // eslint disables because of
 // https://mobx-state-tree.js.org/tips/typescript#using-a-mst-type-at-design-time
-// eslint-disable-next-line @typescript-eslint/no-empty-interface
+// eslint-disable-next-line @typescript-eslint/no-empty-object-type
 export interface OntologyManager extends Instance<typeof OntologyManagerType> {}
-// eslint-disable-next-line @typescript-eslint/no-empty-interface
+// eslint-disable-next-line @typescript-eslint/no-empty-object-type
 export interface OntologyRecord extends Instance<typeof OntologyRecordType> {}
 
 export type OntologyTerm = OntologyDBNode

package/src/SixFrameFeatureDisplay/stateModel.ts

@@ -425,6 +425,6 @@ export type SixFrameFeatureDisplayStateModel = ReturnType<
 >
 // eslint disable because of
 // https://mobx-state-tree.js.org/tips/typescript#using-a-mst-type-at-design-time
-// eslint-disable-next-line @typescript-eslint/no-empty-interface
+// eslint-disable-next-line @typescript-eslint/no-empty-object-type
 export interface SixFrameFeatureDisplay
   extends Instance<SixFrameFeatureDisplayStateModel> {}

package/src/TabularEditor/HybridGrid/HybridGrid.tsx

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/no-unsafe-call */
 import { Menu, MenuItem } from '@jbrowse/core/ui'
 import { useTheme } from '@mui/material'
 import { observer } from 'mobx-react'

package/src/TabularEditor/HybridGrid/NumberCell.tsx

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/unbound-method */
 /* eslint-disable @typescript-eslint/use-unknown-in-catch-callback-variable */
 import { observer } from 'mobx-react'
 import React, { useEffect, useState } from 'react'

package/src/TabularEditor/model.ts

@@ -41,6 +41,6 @@ export const TabularEditorStateModelType = types
 
 // eslint disable because of
 // https://mobx-state-tree.js.org/tips/typescript#using-a-mst-type-at-design-time
-// eslint-disable-next-line @typescript-eslint/no-empty-interface
+// eslint-disable-next-line @typescript-eslint/no-empty-object-type
 export interface TabularEditorStateModel
   extends Instance<typeof TabularEditorStateModelType> {}

package/src/components/AddChildFeature.tsx

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/unbound-method */
 /* eslint-disable @typescript-eslint/no-misused-promises */
 import { AnnotationFeature } from '@apollo-annotation/mst'
 import { AddFeatureChange } from '@apollo-annotation/shared'

package/src/components/AddFeature.tsx

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/unbound-method */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 /* eslint-disable @typescript-eslint/no-misused-promises */
 import { AddFeatureChange } from '@apollo-annotation/shared'
@@ -101,7 +102,6 @@ export function AddFeature({
         break
       }
       default: {
-        // eslint-disable-next-line unicorn/no-useless-undefined
         setStrand(undefined)
       }
     }

package/src/components/AddRefSeqAliases.tsx

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/unbound-method */
 import { ChangeManager } from '../ChangeManager'
 import { ApolloSessionModel } from '../session'
 import { Dialog } from './Dialog'

package/src/components/CopyFeature.tsx

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/unbound-method */
 /* eslint-disable @typescript-eslint/use-unknown-in-catch-callback-variable */
 /* eslint-disable @typescript-eslint/no-unsafe-argument */
 /* eslint-disable @typescript-eslint/no-misused-promises */

package/src/components/DeleteAssembly.tsx

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/unbound-method */
 /* eslint-disable @typescript-eslint/no-misused-promises */
 import { DeleteAssemblyChange } from '@apollo-annotation/shared'
 import { Assembly } from '@jbrowse/core/assemblyManager/assembly'

package/src/components/DeleteFeature.tsx

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/unbound-method */
 /* eslint-disable @typescript-eslint/no-misused-promises */
 import { AnnotationFeature } from '@apollo-annotation/mst'
 import { DeleteFeatureChange } from '@apollo-annotation/shared'

package/src/components/LogOut.tsx

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/unbound-method */
 import {
   Button,
   DialogActions,
@@ -49,7 +50,7 @@ export function LogOut({ handleClose, session }: DeleteAssemblyProps) {
     event.preventDefault()
     setErrorMessage('')
     selectedInternetAccount.removeToken()
-    window.location.reload()
+    globalThis.location.reload()
   }
 
   return (

package/src/components/ManageChecks.tsx

@@ -182,7 +182,7 @@ export function ManageChecks({ handleClose, session }: ManageChecksProps) {
       }
     } else {
       const index = checks.indexOf(_id, 0)
-      if (index > -1) {
+      if (index !== -1) {
         checks.splice(index, 1)
       }
       setSelectedChecks(checks)

package/src/components/ManageUsers.tsx

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/unbound-method */
 /* eslint-disable @typescript-eslint/use-unknown-in-catch-callback-variable */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 /* eslint-disable @typescript-eslint/no-misused-promises */
@@ -154,7 +155,7 @@ export function ManageUsers({
           key={`delete-${params.id}`}
           icon={<DeleteIcon />}
           onClick={async () => {
-            if (window.confirm('Delete this user?')) {
+            if (globalThis.confirm('Delete this user?')) {
               await deleteUser(params.id)
             }
           }}

package/src/components/OntologyTermAutocomplete.tsx

@@ -1,7 +1,7 @@
 /* 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 { AbstractSessionModel } from '@jbrowse/core/util'
+import { isAbortException } from '@jbrowse/core/util/aborting'
 import {
   Autocomplete,
   AutocompleteRenderInputParams,
@@ -76,7 +76,6 @@ export function OntologyTermAutocomplete({
   // effect for clearing choices when not open
   useEffect(() => {
     if (!open) {
-      // eslint-disable-next-line unicorn/no-useless-undefined
       setTermChoices(undefined)
     }
   }, [open])
@@ -93,7 +92,7 @@ export function OntologyTermAutocomplete({
             setCurrentOntologyTerm(term)
           }
         },
-        (error) => {
+        (error: unknown) => {
           if (!signal.aborted && !isAbortException(error)) {
             setCurrentOntologyTermInvalid(String(error))
           }
@@ -116,10 +115,10 @@ export function OntologyTermAutocomplete({
             setTermChoices(soTerms)
           }
         },
-        (error) => {
+        (error: unknown) => {
           if (!signal.aborted && !isAbortException(error)) {
             ;(session as unknown as AbstractSessionModel).notify(
-              error.message,
+              error instanceof Error ? error.message : String(error),
               'error',
             )
           }
@@ -145,7 +144,6 @@ export function OntologyTermAutocomplete({
       return
     }
     if (typeof newValue === 'string') {
-      // eslint-disable-next-line unicorn/no-useless-undefined
       setCurrentOntologyTerm(undefined)
       onChange(valueString, newValue)
     } else if (newValue.lbl !== valueString) {
@@ -212,7 +210,7 @@ async function getCurrentTerm(
     currentTermLabel,
     { includeSubclasses: false },
   )
-  const term = terms.find(filterTerms ?? (() => true))
+  const term = terms.find((term) => (filterTerms ?? (() => true))(term))
   if (!term) {
     throw new Error(`not a valid ${ontologyStore.ontologyName} term`)
   }

package/src/components/OntologyTermMultiSelect.tsx

@@ -1,6 +1,7 @@
+/* eslint-disable @typescript-eslint/unbound-method */
 /* eslint-disable @typescript-eslint/use-unknown-in-catch-callback-variable */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
-import { isAbortException } from '@jbrowse/core/util'
+import { isAbortException } from '@jbrowse/core/util/aborting'
 import {
   Autocomplete,
   AutocompleteRenderGetTagProps,

package/src/components/OpenLocalFile.tsx

@@ -1,3 +1,5 @@
+/* eslint-disable @typescript-eslint/no-unsafe-call */
+/* 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'
@@ -35,7 +37,7 @@ export function OpenLocalFile({ handleClose, session }: OpenLocalFileProps) {
   const { apolloDataStore } = session
   const { addAssembly, addSessionAssembly, assemblyManager, notify } =
     session as unknown as AbstractSessionModel & {
-      // eslint-disable-next-line @typescript-eslint/ban-types
+      // eslint-disable-next-line @typescript-eslint/no-unsafe-function-type
       addSessionAssembly: Function
     }
 

package/src/components/ViewChangeLog.tsx

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/unbound-method */
 /* eslint-disable @typescript-eslint/use-unknown-in-catch-callback-variable */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */

package/src/components/ViewCheckResults.tsx

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/unbound-method */
 /* eslint-disable @typescript-eslint/use-unknown-in-catch-callback-variable */
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
 /* eslint-disable @typescript-eslint/no-unsafe-argument */

package/src/config.ts

@@ -5,6 +5,11 @@ import { OntologyRecordConfiguration } from './OntologyManager'
 
 const ApolloPluginConfigurationSchema = ConfigurationSchema('ApolloPlugin', {
   ontologies: types.array(OntologyRecordConfiguration),
+  featureTypeOntologyName: {
+    description: 'Name of the feature type ontology',
+    type: 'string',
+    defaultValue: 'Sequence Ontology',
+  },
 })
 
 export default ApolloPluginConfigurationSchema

package/src/extensions/annotationFromPileup.ts

@@ -17,7 +17,7 @@ import { ApolloSessionModel } from '../session'
 
 function parseCigar(cigar: string): [string | undefined, number][] {
   return (cigar.toUpperCase().match(/\d+\D/g) ?? []).map((op) => {
-    return [(op.match(/\D/) ?? [])[0], Number.parseInt(op, 10)]
+    return [(/\D/.exec(op) ?? [])[0], Number.parseInt(op, 10)]
   })
 }