@apollo-annotation/jbrowse-plugin-apollo 0.3.11 → 0.3.13

package/src/components/ViewCheckResults.tsx

@@ -4,6 +4,7 @@
 /* eslint-disable @typescript-eslint/no-unsafe-argument */
 /* eslint-disable @typescript-eslint/no-unsafe-member-access */
 /* eslint-disable @typescript-eslint/no-unsafe-return */
+import { getRoot } from '@jbrowse/mobx-state-tree'
 import {
   Button,
   DialogActions,
@@ -19,12 +20,11 @@ import {
   type GridRowsProp,
   GridToolbar,
 } from '@mui/x-data-grid'
-import { getRoot } from 'mobx-state-tree'
 import React, { useEffect, useState } from 'react'
 
-import { type ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
-import { type ApolloSessionModel } from '../session'
-import { type ApolloRootModel } from '../types'
+import type { ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
+import type { ApolloSessionModel } from '../session'
+import type { ApolloRootModel } from '../types'
 import { createFetchErrorMessage } from '../util'
 
 import { Dialog } from './Dialog'

package/src/components/index.ts

@@ -17,3 +17,4 @@ export * from './ViewChangeLog'
 export * from './AddRefSeqAliases'
 export * from './ViewCheckResults'
 export * from './SplitExon'
+export * from './DuplicateTranscript'

package/src/config.ts

@@ -1,5 +1,5 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import { types } from 'mobx-state-tree'
+import { types } from '@jbrowse/mobx-state-tree'
 
 import { OntologyRecordConfiguration } from './OntologyManager'
 

package/src/extensions/annotationFromJBrowseFeature.ts

@@ -3,19 +3,19 @@
 /* eslint-disable @typescript-eslint/no-unsafe-member-access */
 /* eslint-disable @typescript-eslint/no-unsafe-call */
 /* eslint-disable @typescript-eslint/no-unsafe-return */
-import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
+import type { AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
 import { gff3ToAnnotationFeature } from '@apollo-annotation/shared'
-import { type GFF3Feature } from '@gmod/gff'
-import { type Assembly } from '@jbrowse/core/assemblyManager/assembly'
+import type { GFF3Feature } from '@gmod/gff'
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
+import type { PluggableElementType } from '@jbrowse/core/pluggableElementTypes'
 import type DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'
-import type PluggableElementBase from '@jbrowse/core/pluggableElementTypes/PluggableElementBase'
 import {
   type AbstractSessionModel,
   getContainingView,
   getSession,
 } from '@jbrowse/core/util'
-import { type Feature } from '@jbrowse/core/util/simpleFeature'
-import { type LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+import type { Feature } from '@jbrowse/core/util/simpleFeature'
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 import AddIcon from '@mui/icons-material/Add'
 
 import { CreateApolloAnnotation } from '../components/CreateApolloAnnotation'
@@ -24,23 +24,26 @@ function simpleFeatureToGFF3Feature(
   feature: Feature,
   refSeqId: string,
 ): GFF3Feature {
-  // eslint-disable-next-line unicorn/prefer-structured-clone
-  const xfeature = JSON.parse(JSON.stringify(feature))
-  const children = xfeature.subfeatures
+  const children = feature.get('subfeatures')
   const gff3Feature = [
     {
-      start: (xfeature.start as number) + 1,
-      end: xfeature.end as number,
+      start: feature.get('start') + 1,
+      end: feature.get('end'),
       seq_id: refSeqId,
-      source: xfeature.source ?? null,
-      type: xfeature.type ?? null,
-      score: xfeature.score ?? null,
-      strand: xfeature.strand ? (xfeature.strand === 1 ? '+' : '-') : null,
+      source: feature.get('source') ?? null,
+      type: feature.get('type') ?? null,
+      score: feature.get('score') ?? null,
+      strand: feature.get('strand')
+        ? // eslint-disable-next-line unicorn/no-nested-ternary
+          feature.get('strand') === 1
+          ? '+'
+          : '-'
+        : null,
       phase:
-        xfeature.phase !== null || xfeature.phase !== undefined
-          ? (xfeature.phase as string)
+        feature.get('phase') !== null || feature.get('phase') !== undefined
+          ? (feature.get('phase') as string)
           : null,
-      attributes: convertFeatureAttributes(xfeature),
+      attributes: convertFeatureAttributes(feature),
       derived_features: [],
       child_features: children
         ? children.map((x: Feature) => simpleFeatureToGFF3Feature(x, refSeqId))
@@ -71,7 +74,7 @@ function convertFeatureAttributes(feature: Feature): Record<string, string[]> {
     'source',
     'score',
   ])
-  for (const [key, value] of Object.entries(feature)) {
+  for (const [key, value] of Object.entries(feature.toJSON())) {
     if (defaultFields.has(key)) {
       continue
     }
@@ -81,7 +84,7 @@ function convertFeatureAttributes(feature: Feature): Record<string, string[]> {
 }
 
 export function annotationFromJBrowseFeature(
-  pluggableElement: PluggableElementBase,
+  pluggableElement: PluggableElementType,
 ) {
   if (pluggableElement.name !== 'LinearBasicDisplay') {
     return pluggableElement
@@ -124,10 +127,9 @@ export function annotationFromJBrowseFeature(
         }
         return refSeqId
       },
-      getAnnotationFeature(assembly: Assembly) {
+      getAnnotationFeature(assembly: Assembly, feature: Feature) {
         const refSeqId = self.getRefSeqId(assembly)
-        const sfeature: Feature = self.contextMenuFeature.data
-        return jbrowseFeatureToAnnotationFeature(sfeature, refSeqId)
+        return jbrowseFeatureToAnnotationFeature(feature, refSeqId)
       },
     }))
     .views((self) => {
@@ -156,7 +158,10 @@ export function annotationFromJBrowseFeature(
                       handleClose: () => {
                         doneCallback()
                       },
-                      annotationFeature: self.getAnnotationFeature(assembly),
+                      annotationFeature: self.getAnnotationFeature(
+                        assembly,
+                        feature,
+                      ),
                       assembly,
                       refSeqId: self.getRefSeqId(assembly),
                       region,

package/src/extensions/annotationFromPileup.ts

@@ -3,16 +3,18 @@
 /* eslint-disable @typescript-eslint/no-unsafe-member-access */
 /* eslint-disable @typescript-eslint/no-unsafe-call */
 /* eslint-disable @typescript-eslint/no-unsafe-return */
-import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
-import { type Assembly } from '@jbrowse/core/assemblyManager/assembly'
-import { type DisplayType } from '@jbrowse/core/pluggableElementTypes'
-import type PluggableElementBase from '@jbrowse/core/pluggableElementTypes/PluggableElementBase'
+import type { AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
+import type {
+  DisplayType,
+  PluggableElementType,
+} from '@jbrowse/core/pluggableElementTypes'
 import {
   type AbstractSessionModel,
   getContainingView,
   getSession,
 } from '@jbrowse/core/util'
-import { type LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 import AddIcon from '@mui/icons-material/Add'
 import ObjectID from 'bson-objectid'
 
@@ -30,7 +32,7 @@ function parseCigar(cigar: string): [string, number][] {
   return result
 }
 
-export function annotationFromPileup(pluggableElement: PluggableElementBase) {
+export function annotationFromPileup(pluggableElement: PluggableElementType) {
   if (pluggableElement.name !== 'LinearPileupDisplay') {
     return pluggableElement
   }

package/src/index.ts

@@ -1,7 +1,9 @@
 /* eslint-disable @typescript-eslint/unbound-method */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 /* eslint-disable @typescript-eslint/no-misused-promises */
+/* eslint-disable @typescript-eslint/no-explicit-any */
 import { changeRegistry, checkRegistry } from '@apollo-annotation/common'
+import type { AnnotationFeature } from '@apollo-annotation/mst'
 import {
   CDSCheck,
   CoreValidation,
@@ -12,6 +14,7 @@ import {
 } from '@apollo-annotation/shared'
 import Plugin from '@jbrowse/core/Plugin'
 import type PluginManager from '@jbrowse/core/PluginManager'
+import type BaseResult from '@jbrowse/core/TextSearch/BaseResults'
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
 import {
   DisplayType,
@@ -29,7 +32,7 @@ import {
   getSession,
   isAbstractMenuManager,
 } from '@jbrowse/core/util'
-import { type LinearGenomeViewStateModel } from '@jbrowse/plugin-linear-genome-view'
+import type { LinearGenomeViewStateModel } from '@jbrowse/plugin-linear-genome-view'
 import AddIcon from '@mui/icons-material/Add'
 import { alpha } from '@mui/material'
 
@@ -284,6 +287,27 @@ export default class ApolloPlugin extends Plugin {
       'Core-extendPluggableElement',
       annotationFromJBrowseFeature,
     )
+
+    pluginManager.addToExtensionPoint(
+      'LinearGenomeView-searchResultSelected',
+      (_: any, props: Record<string, unknown>) => {
+        const { session, result } = props as {
+          session: ApolloSessionModel
+          result: BaseResult
+        }
+        const trackId = result.getTrackId()
+        const matchedFeature = result.matchedObject
+
+        if (trackId?.startsWith('apollo_track_') && matchedFeature) {
+          const geneFeature = matchedFeature as AnnotationFeature
+          void session.apolloSetEventualSelectedFeature(geneFeature._id)
+        }
+
+        /* eslint-disable-next-line @typescript-eslint/no-unsafe-return */
+        return _
+      },
+    )
+
     if (!inWebWorker) {
       pluginManager.addToExtensionPoint(
         'Core-extendWorker',

package/src/makeDisplayComponent.tsx

@@ -1,18 +1,19 @@
 /* eslint-disable @typescript-eslint/unbound-method */
+
 import { getSession } from '@jbrowse/core/util'
+import { makeStyles } from '@jbrowse/core/util/tss-react'
 import ExpandLessIcon from '@mui/icons-material/ExpandLess'
 import ExpandMoreIcon from '@mui/icons-material/ExpandMore'
 import { Alert, Typography, alpha } from '@mui/material'
 import { observer } from 'mobx-react'
 import React, { useCallback, useEffect, useRef } from 'react'
-import { makeStyles } from 'tss-react/mui'
 
 import { LinearApolloDisplay } from './LinearApolloDisplay/components'
-import { type LinearApolloDisplay as LinearApolloDisplayI } from './LinearApolloDisplay/stateModel'
+import type { LinearApolloDisplay as LinearApolloDisplayI } from './LinearApolloDisplay/stateModel'
 import { LinearApolloSixFrameDisplay } from './LinearApolloSixFrameDisplay/components'
-import { type LinearApolloSixFrameDisplay as LinearApolloSixFrameDisplayI } from './LinearApolloSixFrameDisplay/stateModel'
+import type { LinearApolloSixFrameDisplay as LinearApolloSixFrameDisplayI } from './LinearApolloSixFrameDisplay/stateModel'
 import { TabularEditorPane } from './TabularEditor'
-import { type ApolloSessionModel } from './session'
+import type { ApolloSessionModel } from './session'
 
 const accordionControlHeight = 12
 
@@ -97,7 +98,9 @@ const ResizeHandle = ({
         const controller = new AbortController()
         const { signal } = controller
         function abortDrag() {
-          controller.abort('makeDisplayComponent')
+          controller.abort(
+            new DOMException('Canceling drag event listener', 'AbortError'),
+          )
         }
         globalThis.addEventListener('mousemove', mouseMove, { signal })
         globalThis.addEventListener('mouseup', abortDrag, { signal })

package/src/menus/topLevelMenu.ts

@@ -1,6 +1,6 @@
-import {
-  type AbstractMenuManager,
-  type AbstractSessionModel,
+import type {
+  AbstractMenuManager,
+  AbstractSessionModel,
 } from '@jbrowse/core/util'
 import DownloadIcon from '@mui/icons-material/Download'
 import FactCheckIcon from '@mui/icons-material/FactCheck'
@@ -17,7 +17,7 @@ import {
   ViewChangeLog,
   ViewCheckResults,
 } from '../components'
-import { type ApolloSessionModel } from '../session'
+import type { ApolloSessionModel } from '../session'
 
 export function addTopLevelMenus(rootModel: AbstractMenuManager) {
   rootModel.insertInMenu(

package/src/menus/topLevelMenuAdmin.ts

@@ -1,6 +1,6 @@
-import {
-  type AbstractMenuManager,
-  type AbstractSessionModel,
+import type {
+  AbstractMenuManager,
+  AbstractSessionModel,
 } from '@jbrowse/core/util'
 import AddIcon from '@mui/icons-material/Add'
 import AdminPanelSettingsIcon from '@mui/icons-material/AdminPanelSettings'
@@ -18,7 +18,7 @@ import {
   ManageChecks,
   ManageUsers,
 } from '../components'
-import { type ApolloSessionModel } from '../session'
+import type { ApolloSessionModel } from '../session'
 
 export function addTopLevelAdminMenus(rootModel: AbstractMenuManager) {
   rootModel.appendToMenu('Apollo', {

package/src/session/ClientDataStore.ts

@@ -2,7 +2,7 @@
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 /* eslint-disable @typescript-eslint/no-unsafe-argument */
-import { type ClientDataStore as ClientDataStoreType } from '@apollo-annotation/common'
+import type { ClientDataStore as ClientDataStoreType } from '@apollo-annotation/common'
 import {
   type AnnotationFeatureModel,
   type AnnotationFeatureSnapshot,
@@ -13,14 +13,16 @@ import {
   CheckResult,
   type CheckResultSnapshot,
 } from '@apollo-annotation/mst'
-import { getConf, readConfObject } from '@jbrowse/core/configuration'
-import { type ConfigurationModel } from '@jbrowse/core/configuration/types'
-import { type Region, getSession, isElectron } from '@jbrowse/core/util'
 import {
-  type LocalPathLocation,
-  type UriLocation,
+  type AnyConfigurationModel,
+  getConf,
+  readConfObject,
+} from '@jbrowse/core/configuration'
+import { type Region, getSession, isElectron } from '@jbrowse/core/util'
+import type {
+  LocalPathLocation,
+  UriLocation,
 } from '@jbrowse/core/util/types/mst'
-import { autorun } from 'mobx'
 import {
   type Instance,
   addDisposer,
@@ -29,7 +31,8 @@ import {
   getRoot,
   resolveIdentifier,
   types,
-} from 'mobx-state-tree'
+} from '@jbrowse/mobx-state-tree'
+import { autorun } from 'mobx'
 
 import {
   type ApolloInternetAccount,
@@ -41,13 +44,12 @@ import {
 import { ChangeManager } from '../ChangeManager'
 import {
   OntologyManagerType,
-  type OntologyRecordConfiguration,
   type TextIndexFieldDefinition,
 } from '../OntologyManager'
 import type ApolloPluginConfigurationSchema from '../config'
-import { type ApolloRootModel } from '../types'
+import type { ApolloRootModel } from '../types'
 
-import { type ApolloSessionModel } from './session'
+import type { ApolloSessionModel } from './session'
 
 export function clientDataStoreFactory(
   AnnotationFeatureExtended: typeof AnnotationFeatureModel,
@@ -177,9 +179,7 @@ export function clientDataStoreFactory(
             // take precedence over the ontologies in the configuration.
             const { ontologyManager, pluginConfiguration } = self
             const configuredOntologies =
-              pluginConfiguration.ontologies as ConfigurationModel<
-                typeof OntologyRecordConfiguration
-              >[]
+              pluginConfiguration.ontologies as AnyConfigurationModel[]
             for (const ont of configuredOntologies || []) {
               const [name, version, source, indexFields] = [
                 readConfObject(ont, 'name') as string,
@@ -204,7 +204,12 @@ export function clientDataStoreFactory(
                   statusMessage: `Loading ontology "${name}", version "${version}", this may take a while`,
                   progressPct: 0,
                   cancelCallback: () => {
-                    controller.abort('ClientDataStore')
+                    controller.abort(
+                      new DOMException(
+                        `Canceling loading of ontology "${name}"`,
+                        'AbortError',
+                      ),
+                    )
                     jobsManager.abortJob(job.name)
                   },
                 }

package/src/session/session.ts

@@ -1,7 +1,6 @@
-/* eslint-disable @typescript-eslint/no-unsafe-return */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
-import { type ClientDataStore as ClientDataStoreType } from '@apollo-annotation/common'
+import type { ClientDataStore as ClientDataStoreType } from '@apollo-annotation/common'
 import {
   type AnnotationFeature,
   AnnotationFeatureModel,
@@ -13,16 +12,13 @@ import {
   filterJBrowseConfig,
 } from '@apollo-annotation/shared'
 import type PluginManager from '@jbrowse/core/PluginManager'
-import { type AssemblyModel } from '@jbrowse/core/assemblyManager/assembly'
+import type { AssemblyModel } from '@jbrowse/core/assemblyManager/assembly'
 import { getConf, readConfObject } from '@jbrowse/core/configuration'
-import { type BaseTrackConfig } from '@jbrowse/core/pluggableElementTypes'
-import {
-  type AbstractSessionModel,
-  type SessionWithAddTracks,
+import type { BaseTrackConfig } from '@jbrowse/core/pluggableElementTypes'
+import type {
+  AbstractSessionModel,
+  SessionWithAddTracks,
 } from '@jbrowse/core/util'
-import { type LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
-import SaveIcon from '@mui/icons-material/Save'
-import { autorun, observable } from 'mobx'
 import {
   type Instance,
   type SnapshotOut,
@@ -31,13 +27,16 @@ import {
   getRoot,
   getSnapshot,
   types,
-} from 'mobx-state-tree'
+} from '@jbrowse/mobx-state-tree'
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+import SaveIcon from '@mui/icons-material/Save'
+import { autorun, flow, observable, when } from 'mobx'
 
-import { type ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
+import type { ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
 import { ApolloJobModel } from '../ApolloJobModel'
-import { type ChangeManager } from '../ChangeManager'
+import type { ChangeManager } from '../ChangeManager'
 import type ApolloPluginConfigurationSchema from '../config'
-import { type ApolloRootModel } from '../types'
+import type { ApolloRootModel } from '../types'
 import { createFetchErrorMessage } from '../util'
 
 import { clientDataStoreFactory } from './ClientDataStore'
@@ -207,6 +206,14 @@ export function extendSession(
         }
       },
     }))
+    .actions((self) => ({
+      apolloSetEventualSelectedFeature: flow(
+        function* apolloSetEventualSelectedFeature(featureId: string) {
+          yield when(() => Boolean(self.apolloDataStore.getFeature(featureId)))
+          self.apolloSetSelectedFeature(featureId)
+        },
+      ),
+    }))
     .volatile((self) => ({
       previousSnapshot: getSnapshot(self),
     }))
@@ -338,6 +345,10 @@ export function extendSession(
                   console.error(error)
                   continue
                 }
+                // eslint-disable-next-line @typescript-eslint/no-unsafe-member-access
+                if (!jbrowseConfig.configuration.ApolloPlugin.hasRole) {
+                  continue
+                }
                 // eslint-disable-next-line @typescript-eslint/no-unsafe-call
                 reloadPluginManagerCallback(
                   jbrowseConfig,
@@ -351,7 +362,9 @@ export function extendSession(
         )
       },
       beforeDestroy() {
-        self.abortController.abort('destroying session model')
+        self.abortController.abort(
+          new DOMException('Clean up Apollo session', 'AbortError'),
+        )
       },
     }))
 
@@ -384,10 +397,7 @@ export function extendSession(
                     if (Object.keys(filteredConfig).length === 0) {
                       filteredConfig = undefined
                     }
-                    const trackConfigSnapshot = getSnapshot(conf) as {
-                      trackId: string
-                      type: string
-                    }
+                    const trackConfigSnapshot = getSnapshot(conf)
                     const newTrackId = trackId.slice(
                       0,
                       trackId.length - sessionTrackIdentifier.length,
@@ -405,6 +415,7 @@ export function extendSession(
                         oldJBrowseConfig: filteredConfig,
                         newJBrowseConfig: {
                           ...filteredConfig,
+                          // @ts-expect-error The track types are in the snapshot
                           tracks: filteredConfig?.tracks && [
                             ...filteredConfig.tracks,
                             newTrackConfigSnapshot,

package/src/types.ts

@@ -1,10 +1,16 @@
-import { type BaseInternetAccountModel } from '@jbrowse/core/pluggableElementTypes'
-import { type AppRootModel } from '@jbrowse/core/util'
+import type { BaseInternetAccountModel } from '@jbrowse/core/pluggableElementTypes'
+import type { AppRootModel } from '@jbrowse/core/util'
 
-import { type ApolloInternetAccountModel } from './ApolloInternetAccount/model'
-import { type ApolloSessionModel } from './session'
+import type { ApolloInternetAccountModel } from './ApolloInternetAccount/model'
+import type { ApolloSessionModel } from './session'
 
 export interface ApolloRootModel extends Omit<AppRootModel, 'session'> {
   session: ApolloSessionModel
   internetAccounts: (BaseInternetAccountModel | ApolloInternetAccountModel)[]
 }
+
+export function isApolloInternetAccount(
+  internetAccount: BaseInternetAccountModel | ApolloInternetAccountModel,
+): internetAccount is ApolloInternetAccountModel {
+  return internetAccount.type === 'ApolloInternetAccount'
+}

package/src/util/annotationFeatureUtils.ts

@@ -1,4 +1,4 @@
-import { type AnnotationFeature } from '@apollo-annotation/mst'
+import type { AnnotationFeature } from '@apollo-annotation/mst'
 
 export function getFeatureName(feature: AnnotationFeature) {
   const { attributes } = feature

package/src/util/displayUtils.ts

@@ -1,6 +1,6 @@
-import { type CheckResultIdsType } from '@apollo-annotation/mst'
-import { type Theme } from '@mui/material'
-import { makeStyles } from 'tss-react/mui'
+import type { CheckResultIdsType } from '@apollo-annotation/mst'
+import { makeStyles } from '@jbrowse/core/util/tss-react'
+import type { Theme } from '@mui/material'
 
 export { default as EditZoomThresholdDialog } from '../components/EditZoomThresholdDialog'
 

package/src/util/glyphUtils.ts

@@ -1,24 +1,24 @@
-import {
-  type AnnotationFeature,
-  type TranscriptPartCoding,
+import type {
+  AnnotationFeature,
+  TranscriptPartCoding,
 } from '@apollo-annotation/mst'
-import { type BaseDisplayModel } from '@jbrowse/core/pluggableElementTypes'
-import { type MenuItem } from '@jbrowse/core/ui'
+import type { BaseDisplayModel } from '@jbrowse/core/pluggableElementTypes'
+import type { MenuItem } from '@jbrowse/core/ui'
 import {
   type AbstractSessionModel,
   getContainingView,
   isSessionModelWithWidgets,
 } from '@jbrowse/core/util'
-import { type LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 import SkipNextRoundedIcon from '@mui/icons-material/SkipNextRounded'
 import SkipPreviousRoundedIcon from '@mui/icons-material/SkipPreviousRounded'
 
-import { type LinearApolloDisplayMouseEvents } from '../LinearApolloDisplay/stateModel/mouseEvents'
-import { type LinearApolloSixFrameDisplayMouseEvents } from '../LinearApolloSixFrameDisplay/stateModel/mouseEvents'
+import type { LinearApolloDisplayMouseEvents } from '../LinearApolloDisplay/stateModel/mouseEvents'
+import type { LinearApolloSixFrameDisplayMouseEvents } from '../LinearApolloSixFrameDisplay/stateModel/mouseEvents'
 import { AddChildFeature, CopyFeature, DeleteFeature } from '../components'
-import { type ApolloSessionModel } from '../session'
+import type { ApolloSessionModel } from '../session'
 
-import { type MousePositionWithFeature } from '.'
+import type { MousePositionWithFeature } from '.'
 
 type NavLocation = Parameters<LinearGenomeViewModel['navTo']>[0]
 

package/src/util/index.ts

@@ -1,8 +1,8 @@
-import { getParent } from 'mobx-state-tree'
+import { getParent } from '@jbrowse/mobx-state-tree'
 
-import { type ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
-import { type ApolloSessionModel } from '../session'
-import { type ApolloRootModel } from '../types'
+import type { ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
+import type { ApolloSessionModel } from '../session'
+import type { ApolloRootModel } from '../types'
 
 export async function createFetchErrorMessage(
   response: Response,

package/src/util/loadAssemblyIntoClient.ts

@@ -1,7 +1,7 @@
 import { type ClientDataStore, checkRegistry } from '@apollo-annotation/common'
-import {
-  type ApolloAssemblyI,
-  type CheckResultSnapshot,
+import type {
+  ApolloAssemblyI,
+  CheckResultSnapshot,
 } from '@apollo-annotation/mst'
 import { gff3ToAnnotationFeature } from '@apollo-annotation/shared'
 import {
@@ -10,7 +10,7 @@ import {
   type GFF3Sequence,
   parseStringSync,
 } from '@gmod/gff'
-import { getSnapshot } from 'mobx-state-tree'
+import { getSnapshot } from '@jbrowse/mobx-state-tree'
 
 export async function loadAssemblyIntoClient(
   assemblyId: string,

package/src/util/mouseEventsUtils.ts

@@ -1,5 +1,5 @@
-import { type AnnotationFeature } from '@apollo-annotation/mst'
-import { type LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+import type { AnnotationFeature } from '@apollo-annotation/mst'
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 
 type MinEdge = 'min'
 type MaxEdge = 'max'