@apollo-annotation/jbrowse-plugin-apollo 1.0.0 → 1.1.0

package/src/LinearApolloDisplay/stateModel/layouts.ts

@@ -2,12 +2,12 @@
 
 import type { AnnotationFeature } from '@apollo-annotation/mst'
 import type PluginManager from '@jbrowse/core/PluginManager'
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration'
 import { type AbstractSessionModel, doesIntersect2 } from '@jbrowse/core/util'
 import { addDisposer, isAlive } from '@jbrowse/mobx-state-tree'
 import { autorun, observable } from 'mobx'
 
-import type { ApolloSessionModel } from '../../session'
 import {
   isCDSFeature,
   isExonFeature,
@@ -72,7 +72,9 @@ export function layoutsModelFactory(
       getCanonicalRefName(assemblyName: string, refSeq: string) {
         const { assemblyManager } =
           self.session as unknown as AbstractSessionModel
-        const assembly = assemblyManager.get(assemblyName)
+        const assembly = assemblyManager.get(assemblyName) as
+          | Assembly
+          | undefined
         if (!assembly) {
           throw new Error('no assembly in layout')
         }
@@ -298,9 +300,9 @@ export function layoutsModelFactory(
               }
               // Add features that are in the current view
               for (const region of self.regions) {
-                const assembly = (
-                  self.session as unknown as ApolloSessionModel
-                ).apolloDataStore.assemblies.get(region.assemblyName)
+                const assembly = self.session.apolloDataStore.assemblies.get(
+                  region.assemblyName,
+                )
                 const ref = assembly?.getByRefName(region.refName)
                 const features = ref?.features
                 if (!features) {

package/src/LinearApolloDisplay/stateModel/mouseEvents.ts

@@ -4,6 +4,7 @@ import {
   LocationStartChange,
 } from '@apollo-annotation/shared'
 import type PluginManager from '@jbrowse/core/PluginManager'
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration'
 import type { MenuItem } from '@jbrowse/core/ui'
 import { doesIntersect2 } from '@jbrowse/core/util'
@@ -189,7 +190,9 @@ export function mouseEventsModelFactory(
           }
           const { displayedRegions } = self.lgv
           const region = displayedRegions[start.regionNumber]
-          const assembly = self.getAssemblyId(region.assemblyName)
+          const assembly = self.getAssemblyId(region.assemblyName) as
+            | Assembly
+            | undefined
           const changes = getPropagatedLocationChanges(
             feature,
             current.bp,

package/src/LinearApolloDisplay/stateModel/rendering.ts

@@ -6,8 +6,6 @@ import { type Instance, addDisposer, types } from '@jbrowse/mobx-state-tree'
 import { type Theme, createTheme } from '@mui/material'
 import { autorun } from 'mobx'
 
-import type { ApolloSessionModel } from '../../session'
-
 import { layoutsModelFactory } from './layouts'
 
 export function renderingModelFactory(
@@ -125,9 +123,7 @@ export function renderingModelFactory(
                 self.lgv.dynamicBlocks.totalWidthPx,
                 self.featuresHeight(self.lgv.assemblyNames[0]),
               )
-              for (const collaborator of (
-                self.session as unknown as ApolloSessionModel
-              ).collaborators) {
+              for (const collaborator of self.session.collaborators) {
                 const { locations } = collaborator
                 if (locations.length === 0) {
                   continue

package/src/LinearApolloReferenceSequenceDisplay/stateModel/base.ts

@@ -5,6 +5,7 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import type { AnnotationFeature } from '@apollo-annotation/mst'
 import type PluginManager from '@jbrowse/core/PluginManager'
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import {
   type AnyConfigurationSchemaType,
   ConfigurationReference,
@@ -115,7 +116,9 @@ export function baseModelFactory(
         const { assemblyName } = region
         const { assemblyManager } =
           self.session as unknown as AbstractSessionModel
-        const assembly = assemblyManager.get(assemblyName)
+        const assembly = assemblyManager.get(assemblyName) as
+          | Assembly
+          | undefined
         if (!assembly) {
           throw new Error(`No assembly found with name ${assemblyName}`)
         }
@@ -128,8 +131,7 @@ export function baseModelFactory(
         ) as ApolloInternetAccountModel | undefined
       },
       get changeManager() {
-        return (self.session as unknown as ApolloSessionModel).apolloDataStore
-          .changeManager
+        return self.session.apolloDataStore.changeManager
       },
       getAssemblyId(assemblyName: string) {
         const { assemblyManager } =
@@ -141,12 +143,10 @@ export function baseModelFactory(
         return assembly.name
       },
       get selectedFeature(): AnnotationFeature | undefined {
-        return (self.session as unknown as ApolloSessionModel)
-          .apolloSelectedFeature
+        return self.session.apolloSelectedFeature
       },
       get hoveredFeature(): HoveredFeature | undefined {
-        return (self.session as unknown as ApolloSessionModel)
-          .apolloHoveredFeature
+        return self.session.apolloHoveredFeature
       },
       get height() {
         const { sequenceRowHeight } = self
@@ -232,9 +232,9 @@ export function baseModelFactory(
                 return
               }
               if (self.lgv.bpPerPx <= 3) {
-                void (
-                  self.session as unknown as ApolloSessionModel
-                ).apolloDataStore.loadRefSeq(self.expandedRegions)
+                void self.session.apolloDataStore.loadRefSeq(
+                  self.expandedRegions,
+                )
               }
             },
             {

package/src/LinearApolloSixFrameDisplay/components/LinearApolloSixFrameDisplay.tsx

@@ -3,6 +3,7 @@
 /* eslint-disable @typescript-eslint/no-misused-promises */
 
 import type { CheckResultI } from '@apollo-annotation/mst'
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import { Menu, type MenuItem } from '@jbrowse/core/ui'
 import {
   type AbstractSessionModel,
@@ -157,7 +158,9 @@ export const LinearApolloSixFrameDisplay = observer(
               />
               {lgv.displayedRegions.flatMap((region, idx) => {
                 const widthBp = lgv.bpPerPx * apolloRowHeight
-                const assembly = assemblyManager.get(region.assemblyName)
+                const assembly = assemblyManager.get(region.assemblyName) as
+                  | Assembly
+                  | undefined
                 if (showCheckResults) {
                   const filteredCheckResults = [
                     ...session.apolloDataStore.checkResults.values(),
@@ -187,8 +190,7 @@ export const LinearApolloSixFrameDisplay = observer(
                       })?.offsetPx ?? 0) - lgv.offsetPx
                     const [feature] = checkResult.featureIds
                     if (
-                      !feature ||
-                      !feature.parent ||
+                      !feature?.parent ||
                       !looksLikeGene(feature.parent, session)
                     ) {
                       return null

package/src/LinearApolloSixFrameDisplay/components/TrackLines.tsx

@@ -6,7 +6,7 @@ import type { LinearApolloSixFrameDisplay } from '../stateModel'
 export const TrackLines = observer(function TrackLines({
   model,
   hrStyle = { margin: 0, top: 0, color: 'black' },
-  idx = 0,
+  idx,
 }: {
   model: LinearApolloSixFrameDisplay
   hrStyle?: React.CSSProperties

package/src/LinearApolloSixFrameDisplay/glyphs/GeneGlyph.ts

@@ -2,7 +2,6 @@ import type {
   AnnotationFeature,
   TranscriptPartCoding,
 } from '@apollo-annotation/mst'
-import type { BaseDisplayModel } from '@jbrowse/core/pluggableElementTypes'
 import type { MenuItem } from '@jbrowse/core/ui'
 import {
   type AbstractSessionModel,
@@ -856,7 +855,7 @@ function getContextMenuItems(
     session,
   } = display
   const [region] = regions
-  const currentAssemblyId = display.getAssemblyId(region.assemblyName)
+  const currentAssemblyId = display.getAssemblyId(region.assemblyName) as string
   const menuItems: MenuItem[] = []
   const role = internetAccount ? internetAccount.role : 'admin'
   const readOnly = !(role && ['admin', 'user'].includes(role))
@@ -888,7 +887,7 @@ function getContextMenuItems(
       if (isExonFeature(feature, session)) {
         const adjacentExons = getAdjacentExons(feature, display)
         const lgv = getContainingView(
-          display as BaseDisplayModel,
+          display,
         ) as unknown as LinearGenomeViewModel
         if (adjacentExons.upstream) {
           const exon = adjacentExons.upstream

package/src/LinearApolloSixFrameDisplay/stateModel/base.ts

@@ -5,6 +5,7 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import type { AnnotationFeature } from '@apollo-annotation/mst'
 import type PluginManager from '@jbrowse/core/PluginManager'
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import {
   type AnyConfigurationSchemaType,
   ConfigurationReference,
@@ -128,7 +129,9 @@ export function baseModelFactory(
         const { assemblyName } = region
         const { assemblyManager } =
           self.session as unknown as AbstractSessionModel
-        const assembly = assemblyManager.get(assemblyName)
+        const assembly = assemblyManager.get(assemblyName) as
+          | Assembly
+          | undefined
         if (!assembly) {
           throw new Error(`No assembly found with name ${assemblyName}`)
         }
@@ -141,8 +144,7 @@ export function baseModelFactory(
         ) as ApolloInternetAccountModel | undefined
       },
       get changeManager() {
-        return (self.session as unknown as ApolloSessionModel).apolloDataStore
-          .changeManager
+        return self.session.apolloDataStore.changeManager
       },
       getAssemblyId(assemblyName: string) {
         const { assemblyManager } =
@@ -154,12 +156,10 @@ export function baseModelFactory(
         return assembly.name
       },
       get selectedFeature(): AnnotationFeature | undefined {
-        return (self.session as unknown as ApolloSessionModel)
-          .apolloSelectedFeature
+        return self.session.apolloSelectedFeature
       },
       get hoveredFeature(): HoveredFeature | undefined {
-        return (self.session as unknown as ApolloSessionModel)
-          .apolloHoveredFeature
+        return self.session.apolloHoveredFeature
       },
     }))
     .actions((self) => ({
@@ -294,7 +294,7 @@ export function baseModelFactory(
             {
               label: 'Filter features by type',
               onClick: () => {
-                const session = self.session as unknown as ApolloSessionModel
+                const { session } = self
                 ;(self.session as unknown as AbstractSessionModel).queueDialog(
                   (doneCallback) => [
                     FilterFeatures,
@@ -318,14 +318,10 @@ export function baseModelFactory(
     })
     .actions((self) => ({
       setSelectedFeature(feature?: AnnotationFeature) {
-        ;(
-          self.session as unknown as ApolloSessionModel
-        ).apolloSetSelectedFeature(feature)
+        self.session.apolloSetSelectedFeature(feature)
       },
       setHoveredFeature(hoveredFeature?: HoveredFeature) {
-        ;(
-          self.session as unknown as ApolloSessionModel
-        ).apolloSetHoveredFeature(hoveredFeature)
+        self.session.apolloSetHoveredFeature(hoveredFeature)
       },
       showFeatureDetailsWidget(
         feature: AnnotationFeature,
@@ -363,13 +359,9 @@ export function baseModelFactory(
               if (!self.lgv.initialized || self.regionCannotBeRendered()) {
                 return
               }
-              void (
-                self.session as unknown as ApolloSessionModel
-              ).apolloDataStore.loadFeatures(self.regions)
+              void self.session.apolloDataStore.loadFeatures(self.regions)
               if (self.lgv.bpPerPx <= self.zoomThreshold) {
-                void (
-                  self.session as unknown as ApolloSessionModel
-                ).apolloDataStore.loadRefSeq(self.regions)
+                void self.session.apolloDataStore.loadRefSeq(self.regions)
               }
             },
             { name: 'LinearApolloSixFrameDisplayLoadFeatures', delay: 1000 },

package/src/LinearApolloSixFrameDisplay/stateModel/layouts.ts

@@ -2,6 +2,7 @@
 
 import type { AnnotationFeature } from '@apollo-annotation/mst'
 import type PluginManager from '@jbrowse/core/PluginManager'
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration'
 import {
   type AbstractSessionModel,
@@ -11,7 +12,6 @@ import {
 import { addDisposer, isAlive } from '@jbrowse/mobx-state-tree'
 import { autorun, observable } from 'mobx'
 
-import type { ApolloSessionModel } from '../../session'
 import { looksLikeGene } from '../../util/glyphUtils'
 import { geneGlyph } from '../glyphs/GeneGlyph'
 
@@ -45,7 +45,9 @@ export function layoutsModelFactory(
         const { assemblyManager } =
           self.session as unknown as AbstractSessionModel
         return self.lgv.displayedRegions.map((region) => {
-          const assembly = assemblyManager.get(region.assemblyName)
+          const assembly = assemblyManager.get(region.assemblyName) as
+            | Assembly
+            | undefined
           let min: number | undefined
           let max: number | undefined
           const { end, refName, start } = region
@@ -101,7 +103,9 @@ export function layoutsModelFactory(
         const { assemblyManager } =
           self.session as unknown as AbstractSessionModel
         return self.lgv.displayedRegions.map((region, idx) => {
-          const assembly = assemblyManager.get(region.assemblyName)
+          const assembly = assemblyManager.get(region.assemblyName) as
+            | Assembly
+            | undefined
           const featureLayout = new Map<number, LayoutRow[]>()
           const minMax = self.featuresMinMax[idx]
           if (!minMax) {
@@ -222,9 +226,9 @@ export function layoutsModelFactory(
                 return
               }
               for (const region of self.regions) {
-                const assembly = (
-                  self.session as unknown as ApolloSessionModel
-                ).apolloDataStore.assemblies.get(region.assemblyName)
+                const assembly = self.session.apolloDataStore.assemblies.get(
+                  region.assemblyName,
+                )
                 const ref = assembly?.getByRefName(region.refName)
                 const features = ref?.features
                 if (!features) {

package/src/LinearApolloSixFrameDisplay/stateModel/mouseEvents.ts

@@ -60,53 +60,46 @@ export function mouseEventsModelIntermediateFactory(
         if (!featureTypeOntology) {
           throw new Error('featureTypeOntology is undefined')
         }
-        let foundFeature
-        if (self.geneTrackRowNums.includes(row)) {
-          foundFeature = layoutRow.find(
-            (f) =>
-              f.feature.type == 'exon' &&
-              bp >= f.feature.min &&
-              bp <= f.feature.max,
-          )
-          if (!foundFeature) {
-            foundFeature = layoutRow.find(
-              (f) => bp >= f.feature.min && bp <= f.feature.max,
-            )
-          }
-        } else {
-          foundFeature = layoutRow.find((f) => {
-            const { feature } = f
-            const featureID = feature.attributes.get('gff_id')?.toString()
-            const isTranscript = featureTypeOntology.isTypeOf(
-              feature.type,
-              'transcript',
-            )
-            if (!isTranscript) {
-              return false
-            }
-            for (const loc of feature.cdsLocations) {
-              for (const cds of loc) {
-                const frame = getFrame(
-                  cds.min,
-                  cds.max,
-                  feature.strand ?? 1,
-                  cds.phase,
-                )
-                const frameOffsets = self.showFeatureLabels
-                  ? [0, 5, 3, 1, 15, 13, 11]
-                  : [0, 2, 1, 0, 8, 7, 6]
-                const rowNum = frameOffsets.at(frame)
-                if (row === rowNum && bp >= cds.min && bp <= cds.max) {
-                  return (
-                    featureID === undefined ||
-                    !self.filteredTranscripts.includes(featureID)
+        const foundFeature = self.geneTrackRowNums.includes(row)
+          ? layoutRow.find(
+              (f) =>
+                f.feature.type == 'exon' &&
+                bp >= f.feature.min &&
+                bp <= f.feature.max,
+            ) ??
+            layoutRow.find((f) => bp >= f.feature.min && bp <= f.feature.max)
+          : layoutRow.find((f) => {
+              const { feature } = f
+              const featureID = feature.attributes.get('gff_id')?.toString()
+              const isTranscript = featureTypeOntology.isTypeOf(
+                feature.type,
+                'transcript',
+              )
+              if (!isTranscript) {
+                return false
+              }
+              for (const loc of feature.cdsLocations) {
+                for (const cds of loc) {
+                  const frame = getFrame(
+                    cds.min,
+                    cds.max,
+                    feature.strand ?? 1,
+                    cds.phase,
                   )
+                  const frameOffsets = self.showFeatureLabels
+                    ? [0, 5, 3, 1, 15, 13, 11]
+                    : [0, 2, 1, 0, 8, 7, 6]
+                  const rowNum = frameOffsets.at(frame)
+                  if (row === rowNum && bp >= cds.min && bp <= cds.max) {
+                    return (
+                      featureID === undefined ||
+                      !self.filteredTranscripts.includes(featureID)
+                    )
+                  }
                 }
               }
-            }
-            return false
-          })
-        }
+              return false
+            })
         if (!foundFeature) {
           return mousePosition
         }
@@ -202,7 +195,7 @@ export function mouseEventsModelFactory(
         }
         const { displayedRegions } = self.lgv
         const region = displayedRegions[start.regionNumber]
-        const assembly = self.getAssemblyId(region.assemblyName)
+        const assembly = self.getAssemblyId(region.assemblyName) as string
         const changes = getPropagatedLocationChanges(
           feature,
           current.bp,

package/src/LinearApolloSixFrameDisplay/stateModel/rendering.ts

@@ -11,7 +11,6 @@ import { type Instance, addDisposer, types } from '@jbrowse/mobx-state-tree'
 import { type Theme, createTheme } from '@mui/material'
 import { autorun } from 'mobx'
 
-import type { ApolloSessionModel } from '../../session'
 import { codonColorCode } from '../../util/displayUtils'
 import { looksLikeGene } from '../../util/glyphUtils'
 
@@ -137,9 +136,7 @@ export function renderingModelFactory(
                 self.lgv.dynamicBlocks.totalWidthPx,
                 self.featuresHeight,
               )
-              for (const collaborator of (
-                self.session as unknown as ApolloSessionModel
-              ).collaborators) {
+              for (const collaborator of self.session.collaborators) {
                 const { locations } = collaborator
                 if (locations.length === 0) {
                   continue

package/src/OntologyManager/OntologyStore/fulltext.ts

@@ -10,9 +10,7 @@ import type { OntologyDBNode } from './indexeddb-schema'
 import { applyPrefixes } from './prefixes'
 import type { TextIndexFieldDefinition } from './types'
 
-// eslint-disable-next-line import/no-duplicates
 import type OntologyStore from '.'
-// eslint-disable-next-line import/no-duplicates
 import type { Transaction } from '.'
 
 /** special value of jsonPath that gets the IRI (that is, ID) of the node with the configured prefixes applied */

package/src/OntologyManager/OntologyStore/index.ts

@@ -357,7 +357,7 @@ export default class OntologyStore {
       startingNodes,
       (edge) => edge.pred === subclassRelation,
       direction === 'subclasses' ? 'sub' : 'obj',
-      myTx as unknown as Transaction<['edges']>,
+      myTx,
     )
     for (const n of startingNodes) {
       yield n

package/src/TabularEditor/HybridGrid/ChangeHandling.ts

@@ -18,8 +18,8 @@ export function handleFeatureTypeChange(
     typeName: 'TypeChange',
     changedIds: [featureId],
     featureId,
-    oldType: String(oldType),
-    newType: String(newType),
+    oldType,
+    newType,
     assembly: feature.assemblyId,
   })
   return changeManager.submit(change)

package/src/TabularEditor/HybridGrid/NumberCell.tsx

@@ -1,3 +1,4 @@
+/* eslint-disable @eslint-react/set-state-in-effect */
 /* eslint-disable @typescript-eslint/unbound-method */
 import { makeStyles } from '@jbrowse/core/util/tss-react'
 import { observer } from 'mobx-react'
@@ -41,7 +42,7 @@ export const NumberCell = observer(function NumberCell({
     if (initialValue !== value) {
       setValue(initialValue)
     }
-    // eslint-disable-next-line react-hooks/exhaustive-deps
+    // eslint-disable-next-line @eslint-react/exhaustive-deps
   }, [initialValue])
 
   useEffect(() => {

package/src/components/AddAssemblyAliases.tsx

@@ -59,7 +59,7 @@ export function AddAssemblyAliases({
       id: assembly.name,
       name: assembly.displayName,
       aliases: assembly.aliases.join(', '),
-    } as AssemblyAlias
+    }
   })
 
   const [errorMessage, setErrorMessage] = React.useState('')