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

package/src/OntologyManager/index.ts

@@ -8,7 +8,6 @@ import {
   LocalPathLocation,
   UriLocation,
 } from '@jbrowse/core/util/types/mst'
-import { autorun } from 'mobx'
 import {
   type Instance,
   addDisposer,
@@ -17,13 +16,14 @@ import {
   getSnapshot,
   isAlive,
   types,
-} from 'mobx-state-tree'
+} from '@jbrowse/mobx-state-tree'
+import { autorun } from 'mobx'
 
 import type ApolloPluginConfigurationSchema from '../config'
-import { type ApolloRootModel } from '../types'
+import type { ApolloRootModel } from '../types'
 
 import OntologyStore, { type OntologyStoreOptions } from './OntologyStore'
-import { type OntologyDBNode } from './OntologyStore/indexeddb-schema'
+import type { OntologyDBNode } from './OntologyStore/indexeddb-schema'
 import { applyPrefixes, expandPrefixes } from './OntologyStore/prefixes'
 
 export { isDeprecated } from './OntologyStore/indexeddb-schema'

package/src/OntologyManager/util.ts

@@ -1,4 +1,4 @@
-import { type AnnotationFeature } from '@apollo-annotation/mst'
+import type { AnnotationFeature } from '@apollo-annotation/mst'
 
 import type OntologyStore from './OntologyStore'
 

package/src/TabularEditor/HybridGrid/ChangeHandling.ts

@@ -1,11 +1,11 @@
-import { type AnnotationFeature } from '@apollo-annotation/mst'
+import type { AnnotationFeature } from '@apollo-annotation/mst'
 import {
   LocationEndChange,
   LocationStartChange,
   TypeChange,
 } from '@apollo-annotation/shared'
 
-import { type ChangeManager } from '../../ChangeManager'
+import type { ChangeManager } from '../../ChangeManager'
 
 export function handleFeatureTypeChange(
   changeManager: ChangeManager,

package/src/TabularEditor/HybridGrid/Feature.tsx

@@ -1,17 +1,17 @@
-/* eslint-disable unicorn/no-nested-ternary */
 /* eslint-disable @typescript-eslint/unbound-method */
+/* eslint-disable unicorn/no-nested-ternary */
 
-import { type AnnotationFeature } from '@apollo-annotation/mst'
-import { type AbstractSessionModel } from '@jbrowse/core/util'
+import type { AnnotationFeature } from '@apollo-annotation/mst'
+import type { AbstractSessionModel } from '@jbrowse/core/util'
+import { makeStyles } from '@jbrowse/core/util/tss-react'
 import { observer } from 'mobx-react'
 import React from 'react'
-import { makeStyles } from 'tss-react/mui'
 
 import { isOntologyClass } from '../../OntologyManager'
 import type OntologyStore from '../../OntologyManager/OntologyStore'
 import { OntologyTermAutocomplete } from '../../components/OntologyTermAutocomplete'
 import { navToFeatureCenter } from '../../util'
-import { type DisplayStateModel } from '../types'
+import type { DisplayStateModel } from '../types'
 
 import {
   handleFeatureEndChange,
@@ -19,7 +19,7 @@ import {
   handleFeatureTypeChange,
 } from './ChangeHandling'
 import { FeatureAttributes } from './FeatureAttributes'
-import { type ContextMenuState } from './HybridGrid'
+import type { ContextMenuState } from './HybridGrid'
 import { NumberCell } from './NumberCell'
 import { featureContextMenuItems } from './featureContextMenuItems'
 

package/src/TabularEditor/HybridGrid/FeatureAttributes.tsx

@@ -1,7 +1,7 @@
 /* eslint-disable @typescript-eslint/restrict-template-expressions */
-import { type AnnotationFeature } from '@apollo-annotation/mst'
+import type { AnnotationFeature } from '@apollo-annotation/mst'
+import { getSnapshot } from '@jbrowse/mobx-state-tree'
 import { observer } from 'mobx-react'
-import { getSnapshot } from 'mobx-state-tree'
 import React from 'react'
 
 import Highlight from './Highlight'

package/src/TabularEditor/HybridGrid/Highlight.tsx

@@ -1,5 +1,5 @@
+import { makeStyles } from '@jbrowse/core/util/tss-react'
 import React from 'react'
-import { makeStyles } from 'tss-react/mui'
 
 const useStyles = makeStyles()({
   highlighted: {

package/src/TabularEditor/HybridGrid/HybridGrid.tsx

@@ -1,10 +1,10 @@
 import { Menu, type MenuItem } from '@jbrowse/core/ui'
+import { makeStyles } from '@jbrowse/core/util/tss-react'
 import { useTheme } from '@mui/material'
 import { observer } from 'mobx-react'
 import React, { useEffect, useRef, useState } from 'react'
-import { makeStyles } from 'tss-react/mui'
 
-import { type DisplayStateModel } from '../types'
+import type { DisplayStateModel } from '../types'
 
 import { Feature } from './Feature'
 

package/src/TabularEditor/HybridGrid/NumberCell.tsx

@@ -1,7 +1,7 @@
 /* eslint-disable @typescript-eslint/unbound-method */
+import { makeStyles } from '@jbrowse/core/util/tss-react'
 import { observer } from 'mobx-react'
 import React, { useEffect, useState } from 'react'
-import { makeStyles } from 'tss-react/mui'
 
 const useStyles = makeStyles()((theme) => ({
   inputWrapper: {

package/src/TabularEditor/HybridGrid/ToolBar.tsx

@@ -1,12 +1,13 @@
 /* eslint-disable @typescript-eslint/unbound-method */
+
+import { makeStyles } from '@jbrowse/core/util/tss-react'
 import ClearIcon from '@mui/icons-material/Clear'
 import UnfoldLessIcon from '@mui/icons-material/UnfoldLess'
 import { IconButton, InputAdornment, TextField, Tooltip } from '@mui/material'
 import { observer } from 'mobx-react'
 import React from 'react'
-import { makeStyles } from 'tss-react/mui'
 
-import { type DisplayStateModel } from '../types'
+import type { DisplayStateModel } from '../types'
 
 const useStyles = makeStyles()({
   toolbar: {

package/src/TabularEditor/HybridGrid/featureContextMenuItems.ts

@@ -1,21 +1,22 @@
-import { type AnnotationFeature } from '@apollo-annotation/mst'
-import { type MenuItem } from '@jbrowse/core/ui'
+import type { AnnotationFeature } from '@apollo-annotation/mst'
+import type { MenuItem } from '@jbrowse/core/ui'
 import {
   type AbstractSessionModel,
   type SessionWithWidgets,
   isSessionModelWithWidgets,
 } from '@jbrowse/core/util'
 
-import { type ChangeManager } from '../../ChangeManager'
+import type { ChangeManager } from '../../ChangeManager'
 import {
   AddChildFeature,
   CopyFeature,
   DeleteFeature,
+  DuplicateTranscript,
   MergeExons,
   MergeTranscripts,
   SplitExon,
 } from '../../components'
-import { type ApolloSessionModel } from '../../session'
+import type { ApolloSessionModel } from '../../session'
 import { getApolloInternetAccount } from '../../util'
 
 export function featureContextMenuItems(
@@ -214,6 +215,27 @@ export function featureContextMenuItems(
             session.showWidget(apolloTranscriptWidget)
           },
         },
+        {
+          label: 'Duplicate feature',
+          onClick: () => {
+            ;(session as unknown as AbstractSessionModel).queueDialog(
+              (doneCallback) => [
+                DuplicateTranscript,
+                {
+                  session,
+                  handleClose: () => {
+                    doneCallback()
+                  },
+                  changeManager,
+                  sourceFeature: feature,
+                  sourceAssemblyId: currentAssemblyId,
+                  selectedFeature,
+                  setSelectedFeature,
+                },
+              ],
+            )
+          },
+        },
         {
           label: 'Visible',
           type: 'checkbox',

package/src/TabularEditor/TabularEditorPane.tsx

@@ -3,7 +3,7 @@ import React from 'react'
 
 import HybridGrid from './HybridGrid'
 import { ToolBar } from './HybridGrid/ToolBar'
-import { type DisplayStateModel } from './types'
+import type { DisplayStateModel } from './types'
 
 function stopPropagation(e: React.MouseEvent) {
   e.stopPropagation()

package/src/TabularEditor/model.ts

@@ -1,6 +1,6 @@
-import { type Instance, getParent, types } from 'mobx-state-tree'
+import { type Instance, getParent, types } from '@jbrowse/mobx-state-tree'
 
-import { type DisplayStateModel } from './types'
+import type { DisplayStateModel } from './types'
 
 export const TabularEditorStateModelType = types
   .model('TabularEditor', {

package/src/TabularEditor/types.ts

@@ -1,5 +1,5 @@
-import { type LinearApolloDisplay } from '../LinearApolloDisplay/stateModel'
-import { type LinearApolloSixFrameDisplay } from '../LinearApolloSixFrameDisplay/stateModel'
+import type { LinearApolloDisplay } from '../LinearApolloDisplay/stateModel'
+import type { LinearApolloSixFrameDisplay } from '../LinearApolloSixFrameDisplay/stateModel'
 
 export type DisplayStateModel =
   | LinearApolloDisplay

package/src/components/AddAssembly.tsx

@@ -1,5 +1,5 @@
 /* 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 */
@@ -9,7 +9,9 @@ import {
   AddAssemblyFromFileChange,
 } from '@apollo-annotation/shared'
 import { readConfObject } from '@jbrowse/core/configuration'
-import { type AbstractSessionModel } from '@jbrowse/core/util'
+import type { AbstractSessionModel } from '@jbrowse/core/util'
+import { makeStyles } from '@jbrowse/core/util/tss-react'
+import { getRoot } from '@jbrowse/mobx-state-tree'
 import InfoIcon from '@mui/icons-material/Info'
 import LinkIcon from '@mui/icons-material/Link'
 import RadioButtonCheckedIcon from '@mui/icons-material/RadioButtonChecked'
@@ -26,6 +28,7 @@ import {
   DialogContentText,
   FormControlLabel,
   FormGroup,
+  FormHelperText,
   IconButton,
   InputAdornment,
   LinearProgress,
@@ -38,14 +41,12 @@ import {
   Typography,
 } from '@mui/material'
 import ObjectID from 'bson-objectid'
-import { getRoot } from 'mobx-state-tree'
 import React, { useState } from 'react'
-import { makeStyles } from 'tss-react/mui'
 
-import { type ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
-import { type ChangeManager } from '../ChangeManager'
-import { type ApolloSessionModel } from '../session'
-import { type ApolloRootModel } from '../types'
+import type { ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
+import type { ChangeManager } from '../ChangeManager'
+import type { ApolloSessionModel } from '../session'
+import type { ApolloRootModel } from '../types'
 import { createFetchErrorMessage } from '../util'
 
 import { Dialog } from './Dialog'
@@ -139,6 +140,7 @@ export function AddAssembly({
   const [importFeatures, setImportFeatures] = useState(true)
   const [sequenceIsEditable, setSequenceIsEditable] = useState(false)
   const [submitted, setSubmitted] = useState(false)
+  const [strict, setStrict] = useState(true)
 
   const [fastaFile, setFastaFile] = useState<File | null>(null)
   const [fastaIndexFile, setFastaIndexFile] = useState<File | null>(null)
@@ -194,42 +196,42 @@ export function AddAssembly({
       locationType: 'UriLocation',
       uri,
     })
-    if (apolloFetchFile) {
-      const job = {
-        name: `UploadAssemblyFile for ${assemblyName}`,
-        statusMessage: 'Pre-validating',
-        progressPct: 0,
-        cancelCallback: () => {
-          controller.abort('AddAssembly')
-          jobsManager.abortJob(job.name)
-        },
-      }
-      jobsManager.runJob(job)
-      jobsManager.update(
-        job.name,
-        `Uploading ${file.name}, this may take awhile`,
-      )
-      const { signal } = controller
-
-      const response = await apolloFetchFile(uri, {
-        method: 'POST',
-        body: formData,
-        signal,
-      })
-      if (!response.ok) {
-        const newErrorMessage = await createFetchErrorMessage(
-          response,
-          'Error when inserting new assembly (while uploading file)',
+    const job = {
+      name: `UploadAssemblyFile for ${assemblyName}`,
+      statusMessage: 'Pre-validating',
+      progressPct: 0,
+      cancelCallback: () => {
+        controller.abort(
+          new DOMException(
+            `Canceling adding of assembly "${assemblyName}"`,
+            'AbortError',
+          ),
         )
-        jobsManager.abortJob(job.name, newErrorMessage)
-        setErrorMessage(newErrorMessage)
-        return ''
-      }
-      const result = await response.json()
-      const fileId = result._id as string
-      jobsManager.done(job)
-      return fileId
+        jobsManager.abortJob(job.name)
+      },
     }
+    jobsManager.runJob(job)
+    jobsManager.update(job.name, `Uploading ${file.name}, this may take awhile`)
+    const { signal } = controller
+
+    const response = await apolloFetchFile(uri, {
+      method: 'POST',
+      body: formData,
+      signal,
+    })
+    if (!response.ok) {
+      const newErrorMessage = await createFetchErrorMessage(
+        response,
+        'Error when inserting new assembly (while uploading file)',
+      )
+      jobsManager.abortJob(job.name, newErrorMessage)
+      setErrorMessage(newErrorMessage)
+      return ''
+    }
+    const result = await response.json()
+    const fileId = result._id as string
+    jobsManager.done(job)
+    return fileId
     throw new Error('Failed to fetch')
   }
 
@@ -270,6 +272,7 @@ export function AddAssembly({
           assembly: new ObjectID().toHexString(),
           assemblyName,
           fileIds: { fa: faId },
+          parseOptions: { strict },
         })
       } else if (fileType === FileType.GFF3) {
         const faId = await uploadFile(fastaFile, FileType.GFF3)
@@ -740,6 +743,22 @@ export function AddAssembly({
                     }
                     label="Load features from GFF3 file"
                   />
+                  <FormControlLabel
+                    label="Strict parsing"
+                    disabled={!importFeatures || (submitted && !errorMessage)}
+                    control={
+                      <Checkbox
+                        checked={strict}
+                        onChange={(e: React.ChangeEvent<HTMLInputElement>) => {
+                          setStrict(e.target.checked)
+                        }}
+                      />
+                    }
+                  />
+                  <FormHelperText>
+                    Don&apos;t import any features if any lines in the GFF3 are
+                    unable to be processed
+                  </FormHelperText>
                   <FormControlLabel
                     data-testid="gff3-is-gzip-checkbox"
                     control={

package/src/components/AddAssemblyAliases.tsx

@@ -3,12 +3,12 @@ import { Box, DialogContent, DialogContentText } from '@mui/material'
 import { DataGrid, type GridColDef, type GridRowModel } from '@mui/x-data-grid'
 import React from 'react'
 
-import {
-  type ApolloInternetAccount,
-  type CollaborationServerDriver,
+import type {
+  ApolloInternetAccount,
+  CollaborationServerDriver,
 } from '../BackendDrivers'
-import { type ChangeManager } from '../ChangeManager'
-import { type ApolloSessionModel } from '../session'
+import type { ChangeManager } from '../ChangeManager'
+import type { ApolloSessionModel } from '../session'
 
 import { Dialog } from './Dialog'
 

package/src/components/AddChildFeature.tsx

@@ -1,6 +1,6 @@
 /* eslint-disable @typescript-eslint/unbound-method */
 
-import { type AnnotationFeature } from '@apollo-annotation/mst'
+import type { AnnotationFeature } from '@apollo-annotation/mst'
 import { AddFeatureChange } from '@apollo-annotation/shared'
 import {
   Button,
@@ -12,11 +12,11 @@ import {
 import ObjectID from 'bson-objectid'
 import React, { useState } from 'react'
 
-import { type ChangeManager } from '../ChangeManager'
+import type { ChangeManager } from '../ChangeManager'
 import { isOntologyClass } from '../OntologyManager'
 import type OntologyStore from '../OntologyManager/OntologyStore'
 import { fetchValidDescendantTerms } from '../OntologyManager/util'
-import { type ApolloSessionModel } from '../session'
+import type { ApolloSessionModel } from '../session'
 
 import { Dialog } from './Dialog'
 import { OntologyTermAutocomplete } from './OntologyTermAutocomplete'

package/src/components/AddFeature.tsx

@@ -1,8 +1,8 @@
 /* eslint-disable @typescript-eslint/unbound-method */
 
-import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
+import type { AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
 import { AddFeatureChange } from '@apollo-annotation/shared'
-import { type Region } from '@jbrowse/core/util/types'
+import type { Region } from '@jbrowse/core/util/types'
 import InfoIcon from '@mui/icons-material/Info'
 import {
   Box,
@@ -26,9 +26,9 @@ import ObjectID from 'bson-objectid'
 import React, { useState } from 'react'
 
 import { CollaborationServerDriver } from '../BackendDrivers'
-import { type ChangeManager } from '../ChangeManager'
+import type { ChangeManager } from '../ChangeManager'
 import { isOntologyClass } from '../OntologyManager'
-import { type ApolloSessionModel } from '../session'
+import type { ApolloSessionModel } from '../session'
 
 import { Dialog } from './Dialog'
 import { OntologyTermAutocomplete } from './OntologyTermAutocomplete'

package/src/components/AddRefSeqAliases.tsx

@@ -3,7 +3,7 @@ import {
   AddRefSeqAliasesChange,
   type SerializedRefSeqAliases,
 } from '@apollo-annotation/shared'
-import { type Assembly } from '@jbrowse/core/assemblyManager/assembly'
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import {
   Button,
   DialogActions,
@@ -25,13 +25,13 @@ import {
 import { observer } from 'mobx-react'
 import React, { useEffect, useRef, useState } from 'react'
 
-import {
-  type ApolloInternetAccount,
-  type CollaborationServerDriver,
-  type RefNameAliases,
+import type {
+  ApolloInternetAccount,
+  CollaborationServerDriver,
+  RefNameAliases,
 } from '../BackendDrivers'
-import { type ChangeManager } from '../ChangeManager'
-import { type ApolloSessionModel } from '../session'
+import type { ChangeManager } from '../ChangeManager'
+import type { ApolloSessionModel } from '../session'
 
 import { Dialog } from './Dialog'
 

package/src/components/CopyFeature.tsx

@@ -3,13 +3,14 @@
 /* eslint-disable @typescript-eslint/no-unsafe-argument */
 /* eslint-disable @typescript-eslint/no-misused-promises */
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
-import {
-  type AnnotationFeature,
-  type AnnotationFeatureSnapshot,
+import type {
+  AnnotationFeature,
+  AnnotationFeatureSnapshot,
 } from '@apollo-annotation/mst'
 import { AddFeatureChange } from '@apollo-annotation/shared'
 import { readConfObject } from '@jbrowse/core/configuration'
-import { type AbstractSessionModel } from '@jbrowse/core/util'
+import type { AbstractSessionModel } from '@jbrowse/core/util'
+import { getSnapshot } from '@jbrowse/mobx-state-tree'
 import {
   Button,
   DialogActions,
@@ -21,12 +22,11 @@ import {
   TextField,
 } from '@mui/material'
 import ObjectID from 'bson-objectid'
-import { type IKeyValueMap } from 'mobx'
-import { getSnapshot } from 'mobx-state-tree'
+import type { IKeyValueMap } from 'mobx'
 import React, { useEffect, useState } from 'react'
 
-import { type ChangeManager } from '../ChangeManager'
-import { type ApolloSessionModel } from '../session'
+import type { ChangeManager } from '../ChangeManager'
+import type { ApolloSessionModel } from '../session'
 
 import { Dialog } from './Dialog'
 

package/src/components/CreateApolloAnnotation.tsx

@@ -2,14 +2,15 @@
 /* eslint-disable @typescript-eslint/no-misused-promises */
 /* eslint-disable @typescript-eslint/unbound-method */
 
-import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
+import type { AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
 import {
   AddFeatureChange,
   LocationEndChange,
   LocationStartChange,
 } from '@apollo-annotation/shared'
-import { type Assembly } from '@jbrowse/core/assemblyManager/assembly'
-import { type AbstractSessionModel } from '@jbrowse/core/util'
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
+import type { AbstractSessionModel } from '@jbrowse/core/util'
+import { getSnapshot } from '@jbrowse/mobx-state-tree'
 import {
   Box,
   Button,
@@ -26,10 +27,9 @@ import {
   Typography,
 } from '@mui/material'
 import ObjectID from 'bson-objectid'
-import { getSnapshot } from 'mobx-state-tree'
 import React, { useEffect, useMemo, useState } from 'react'
 
-import { type ApolloSessionModel } from '../session'
+import type { ApolloSessionModel } from '../session'
 
 import { Dialog } from './Dialog'
 

package/src/components/DeleteAssembly.tsx

@@ -1,6 +1,7 @@
 /* eslint-disable @typescript-eslint/unbound-method */
 /* eslint-disable @typescript-eslint/no-misused-promises */
 import { DeleteAssemblyChange } from '@apollo-annotation/shared'
+import { getRoot } from '@jbrowse/mobx-state-tree'
 import {
   Button,
   Checkbox,
@@ -13,17 +14,16 @@ import {
   Select,
   type SelectChangeEvent,
 } from '@mui/material'
-import { getRoot } from 'mobx-state-tree'
 import React, { useState } from 'react'
 
-import { type ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
-import {
-  type ApolloInternetAccount,
-  type CollaborationServerDriver,
+import type { ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
+import type {
+  ApolloInternetAccount,
+  CollaborationServerDriver,
 } from '../BackendDrivers'
-import { type ChangeManager } from '../ChangeManager'
-import { type ApolloSessionModel } from '../session'
-import { type ApolloRootModel } from '../types'
+import type { ChangeManager } from '../ChangeManager'
+import type { ApolloSessionModel } from '../session'
+import type { ApolloRootModel } from '../types'
 
 import { Dialog } from './Dialog'
 

package/src/components/DeleteFeature.tsx

@@ -1,22 +1,22 @@
 /* eslint-disable @typescript-eslint/unbound-method */
 
-import { type AnnotationFeature } from '@apollo-annotation/mst'
+import type { AnnotationFeature } from '@apollo-annotation/mst'
 import {
   DeleteFeatureChange,
   LocationEndChange,
   LocationStartChange,
 } from '@apollo-annotation/shared'
+import { getSnapshot } from '@jbrowse/mobx-state-tree'
 import {
   Button,
   DialogActions,
   DialogContent,
   DialogContentText,
 } from '@mui/material'
-import { getSnapshot } from 'mobx-state-tree'
 import React, { useState } from 'react'
 
-import { type ChangeManager } from '../ChangeManager'
-import { type ApolloSessionModel } from '../session'
+import type { ChangeManager } from '../ChangeManager'
+import type { ApolloSessionModel } from '../session'
 
 import { Dialog } from './Dialog'
 

package/src/components/Dialog.tsx

@@ -1,10 +1,10 @@
 /* eslint-disable @typescript-eslint/unbound-method */
 import { Dialog as JBDialog } from '@jbrowse/core/ui'
+import { makeStyles } from '@jbrowse/core/util/tss-react'
 import CloseIcon from '@mui/icons-material/Close'
 import { type DialogProps, DialogTitle, IconButton } from '@mui/material'
 import { observer } from 'mobx-react'
 import React from 'react'
-import { makeStyles } from 'tss-react/mui'
 
 const useStyles = makeStyles()((theme) => ({
   dialogTitle: {

package/src/components/DownloadGFF3.tsx

@@ -3,11 +3,12 @@
 /* eslint-disable @typescript-eslint/no-unsafe-member-access */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 /* eslint-disable @typescript-eslint/no-misused-promises */
-import { type ApolloAssembly } from '@apollo-annotation/mst'
+import type { ApolloAssembly } from '@apollo-annotation/mst'
 import { annotationFeatureToGFF3 } from '@apollo-annotation/shared'
 import { type GFF3Item, formatSync } from '@gmod/gff'
-import { type Assembly } from '@jbrowse/core/assemblyManager/assembly'
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import { getConf } from '@jbrowse/core/configuration'
+import { type IMSTMap, getSnapshot } from '@jbrowse/mobx-state-tree'
 import {
   Button,
   Checkbox,
@@ -21,15 +22,14 @@ import {
   type SelectChangeEvent,
 } from '@mui/material'
 import { saveAs } from 'file-saver'
-import { type IMSTMap, getSnapshot } from 'mobx-state-tree'
 import React, { useState } from 'react'
 
-import {
-  type ApolloInternetAccount,
-  type CollaborationServerDriver,
-  type InMemoryFileDriver,
+import type {
+  ApolloInternetAccount,
+  CollaborationServerDriver,
+  InMemoryFileDriver,
 } from '../BackendDrivers'
-import { type ApolloSessionModel } from '../session'
+import type { ApolloSessionModel } from '../session'
 import { createFetchErrorMessage } from '../util'
 
 import { Dialog } from './Dialog'