@apollo-annotation/jbrowse-plugin-apollo 0.3.11 → 0.3.12

package/src/LinearApolloDisplay/stateModel/rendering.ts

@@ -1,12 +1,12 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import type PluginManager from '@jbrowse/core/PluginManager'
-import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration'
 import { doesIntersect2 } from '@jbrowse/core/util'
+import { type Instance, addDisposer, types } from '@jbrowse/mobx-state-tree'
 import { type Theme, createTheme } from '@mui/material'
 import { autorun } from 'mobx'
-import { type Instance, addDisposer, types } from 'mobx-state-tree'
 
-import { type ApolloSessionModel } from '../../session'
+import type { ApolloSessionModel } from '../../session'
 
 import { layoutsModelFactory } from './layouts'
 

package/src/LinearApolloReferenceSequenceDisplay/components/LinearApolloReferenceSequenceDisplay.tsx

@@ -1,13 +1,14 @@
 /* eslint-disable @typescript-eslint/unbound-method */
+
 /* eslint-disable @typescript-eslint/no-misused-promises */
 import { getContainingView } from '@jbrowse/core/util'
-import { type LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 import { Alert, Tooltip, useTheme } from '@mui/material'
 import { observer } from 'mobx-react'
 import React, { useEffect } from 'react'
 
 import { useStyles } from '../../util/displayUtils'
-import { type LinearApolloReferenceSequenceDisplay as LinearApolloReferenceSequenceDisplayI } from '../stateModel'
+import type { LinearApolloReferenceSequenceDisplay as LinearApolloReferenceSequenceDisplayI } from '../stateModel'
 
 interface LinearApolloReferenceSequenceDisplayProps {
   model: LinearApolloReferenceSequenceDisplayI
@@ -34,6 +35,7 @@ export const LinearApolloReferenceSequenceDisplay = observer(
     const lgv = getContainingView(model) as unknown as LinearGenomeViewModel
     const message = regionCannotBeRendered()
 
+    // This type is wrong in @jbrowse/core
     // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
     if (message) {
       return (

package/src/LinearApolloReferenceSequenceDisplay/drawSequenceOverlay.ts

@@ -1,9 +1,9 @@
-import { type AnnotationFeature } from '@apollo-annotation/mst'
+import type { AnnotationFeature } from '@apollo-annotation/mst'
 import { type Frame, getFrame } from '@jbrowse/core/util'
-import { type BlockSet, type ContentBlock } from '@jbrowse/core/util/blockTypes'
-import { type Theme } from '@mui/material'
+import type { BlockSet, ContentBlock } from '@jbrowse/core/util/blockTypes'
+import type { Theme } from '@mui/material'
 
-import { type ApolloSessionModel, type HoveredFeature } from '../session'
+import type { ApolloSessionModel, HoveredFeature } from '../session'
 
 function getSeqRow(
   strand: 1 | -1 | undefined,

package/src/LinearApolloReferenceSequenceDisplay/drawSequenceTrack.ts

@@ -1,9 +1,9 @@
 import { defaultCodonTable, getFrame, revcom } from '@jbrowse/core/util'
-import { type BlockSet } from '@jbrowse/core/util/blockTypes'
-import { type Theme } from '@mui/material'
+import type { BlockSet } from '@jbrowse/core/util/blockTypes'
+import type { Theme } from '@mui/material'
 
 import { strokeRectInner } from '../LinearApolloDisplay/glyphs/util'
-import { type ApolloSessionModel } from '../session'
+import type { ApolloSessionModel } from '../session'
 import { codonColorCode, colorCode } from '../util/displayUtils'
 
 function drawLetter(

package/src/LinearApolloReferenceSequenceDisplay/stateModel/base.ts

@@ -3,10 +3,13 @@
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
 /* eslint-disable @typescript-eslint/no-unsafe-member-access */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
-import { type AnnotationFeature } from '@apollo-annotation/mst'
+import type { AnnotationFeature } from '@apollo-annotation/mst'
 import type PluginManager from '@jbrowse/core/PluginManager'
-import { ConfigurationReference, getConf } from '@jbrowse/core/configuration'
-import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
+import {
+  type AnyConfigurationSchemaType,
+  ConfigurationReference,
+  getConf,
+} from '@jbrowse/core/configuration'
 import { BaseDisplay } from '@jbrowse/core/pluggableElementTypes'
 import {
   type AbstractSessionModel,
@@ -15,13 +18,13 @@ import {
 } from '@jbrowse/core/util'
 import { getParentRenderProps } from '@jbrowse/core/util/tracks'
 // import type LinearGenomeViewPlugin from '@jbrowse/plugin-linear-genome-view'
-import { type LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+import { addDisposer, getRoot, types } from '@jbrowse/mobx-state-tree'
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 import { autorun } from 'mobx'
-import { addDisposer, getRoot, types } from 'mobx-state-tree'
 
-import { type ApolloInternetAccountModel } from '../../ApolloInternetAccount/model'
-import { type ApolloSessionModel, type HoveredFeature } from '../../session'
-import { type ApolloRootModel } from '../../types'
+import type { ApolloInternetAccountModel } from '../../ApolloInternetAccount/model'
+import type { ApolloSessionModel, HoveredFeature } from '../../session'
+import type { ApolloRootModel } from '../../types'
 
 const minDisplayHeight = 20
 

package/src/LinearApolloReferenceSequenceDisplay/stateModel/index.ts

@@ -1,6 +1,6 @@
 import type PluginManager from '@jbrowse/core/PluginManager'
-import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
-import { type Instance } from 'mobx-state-tree'
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration'
+import type { Instance } from '@jbrowse/mobx-state-tree'
 
 import { renderingModelFactory } from './rendering'
 

package/src/LinearApolloReferenceSequenceDisplay/stateModel/rendering.ts

@@ -1,9 +1,9 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import type PluginManager from '@jbrowse/core/PluginManager'
-import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration'
+import { type Instance, addDisposer } from '@jbrowse/mobx-state-tree'
 import { type Theme, createTheme } from '@mui/material'
 import { autorun } from 'mobx'
-import { type Instance, addDisposer } from 'mobx-state-tree'
 
 import { drawSequenceOverlay } from '../drawSequenceOverlay'
 import { drawSequenceTrack } from '../drawSequenceTrack'

package/src/LinearApolloSixFrameDisplay/components/LinearApolloSixFrameDisplay.tsx

@@ -1,7 +1,8 @@
 /* eslint-disable @typescript-eslint/unbound-method */
+
 /* eslint-disable @typescript-eslint/no-misused-promises */
-/* eslint-disable @typescript-eslint/no-unnecessary-condition */
-import { type CheckResultI } from '@apollo-annotation/mst'
+
+import type { CheckResultI } from '@apollo-annotation/mst'
 import { Menu, type MenuItem } from '@jbrowse/core/ui'
 import {
   type AbstractSessionModel,
@@ -9,7 +10,7 @@ import {
   getContainingView,
   getFrame,
 } from '@jbrowse/core/util'
-import { type LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 import ErrorIcon from '@mui/icons-material/Error'
 import LockIcon from '@mui/icons-material/Lock'
 import { Alert, Avatar, Badge, Box, Tooltip, useTheme } from '@mui/material'
@@ -21,7 +22,7 @@ import {
   clusterResultByMessage,
   useStyles,
 } from '../../util/displayUtils'
-import { type LinearApolloSixFrameDisplay as LinearApolloSixFrameDisplayI } from '../stateModel'
+import type { LinearApolloSixFrameDisplay as LinearApolloSixFrameDisplayI } from '../stateModel'
 
 import { TrackLines } from './TrackLines'
 
@@ -41,7 +42,6 @@ export const LinearApolloSixFrameDisplay = observer(
       contextMenuItems: getContextMenuItems,
       cursor,
       featuresHeight,
-      featureLabelSpacer,
       geneTrackRowNums,
       isShown,
       onMouseDown,
@@ -55,6 +55,7 @@ export const LinearApolloSixFrameDisplay = observer(
       setOverlayCanvas,
       setTheme,
       showCheckResults,
+      showFeatureLabels,
     } = model
     const { classes } = useStyles()
     const lgv = getContainingView(model) as unknown as LinearGenomeViewModel
@@ -64,6 +65,7 @@ export const LinearApolloSixFrameDisplay = observer(
     }, [theme, setTheme])
     const [contextCoord, setContextCoord] = useState<Coord>()
     const [contextMenuItems, setContextMenuItems] = useState<MenuItem[]>([])
+
     const message = regionCannotBeRendered()
     if (!isShown) {
       return null
@@ -94,6 +96,8 @@ export const LinearApolloSixFrameDisplay = observer(
               <LockIcon />
             </div>
           ) : null}
+          {/* This type is wrong in @jbrowse/core */}
+          {/* eslint-disable-next-line @typescript-eslint/no-unnecessary-condition */}
           {message ? (
             <Alert
               severity="warning"
@@ -188,15 +192,19 @@ export const LinearApolloSixFrameDisplay = observer(
                     let row
                     for (const loc of feature.cdsLocations) {
                       for (const cds of loc) {
-                        let rowNum: number = getFrame(
+                        const frame = getFrame(
                           cds.min,
                           cds.max,
                           feature.strand ?? 1,
                           cds.phase,
                         )
-                        rowNum = featureLabelSpacer(
-                          rowNum < 0 ? -1 * rowNum + 5 : rowNum,
-                        )
+                        const frameOffsets = showFeatureLabels
+                          ? [0, 5, 3, 1, 15, 13, 11]
+                          : [0, 2, 1, 0, 8, 7, 6]
+                        const rowNum = frameOffsets.at(frame)
+                        if (!rowNum) {
+                          continue
+                        }
                         if (
                           checkResult.start >= cds.min &&
                           checkResult.start <= cds.max

package/src/LinearApolloSixFrameDisplay/components/TrackLines.tsx

@@ -1,7 +1,7 @@
 import { observer } from 'mobx-react'
 import React from 'react'
 
-import { type LinearApolloSixFrameDisplay } from '../stateModel'
+import type { LinearApolloSixFrameDisplay } from '../stateModel'
 
 export const TrackLines = observer(function TrackLines({
   model,

package/src/LinearApolloSixFrameDisplay/glyphs/GeneGlyph.ts

@@ -1,9 +1,9 @@
-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,
@@ -11,10 +11,10 @@ import {
   intersection2,
   measureText,
 } from '@jbrowse/core/util'
-import { type LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+import { getSnapshot } from '@jbrowse/mobx-state-tree'
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 import { alpha } from '@mui/material'
 import equal from 'fast-deep-equal/es6'
-import { getSnapshot } from 'mobx-state-tree'
 
 import { MergeExons, SplitExon } from '../../components'
 import { FilterTranscripts } from '../../components/FilterTranscripts'
@@ -35,12 +35,12 @@ import {
   navToFeatureCenter,
   selectFeatureAndOpenWidget,
 } from '../../util'
-import { type LinearApolloSixFrameDisplay } from '../stateModel'
-import { type LinearApolloSixFrameDisplayMouseEvents } from '../stateModel/mouseEvents'
-import { type LinearApolloSixFrameDisplayRendering } from '../stateModel/rendering'
-import { type CanvasMouseEvent } from '../types'
+import type { LinearApolloSixFrameDisplay } from '../stateModel'
+import type { LinearApolloSixFrameDisplayMouseEvents } from '../stateModel/mouseEvents'
+import type { LinearApolloSixFrameDisplayRendering } from '../stateModel/rendering'
+import type { CanvasMouseEvent } from '../types'
 
-import { type Glyph } from './Glyph'
+import type { Glyph } from './Glyph'
 
 let forwardFillLight: CanvasPattern | null = null
 let backwardFillLight: CanvasPattern | null = null
@@ -347,9 +347,14 @@ function draw(
           cdsStartPx = reversed ? minX - cdsWidthPx : minX
           ctx.fillStyle = theme.palette.text.primary
           const frame = getFrame(cds.min, cds.max, child.strand ?? 1, cds.phase)
-          const frameAdjust =
-            (frame < 0 ? -1 * frame + 5 : frame) * featureLabelSpacer
-          cdsTop = (frameAdjust - featureLabelSpacer) * rowHeight
+          const frameOffsets = showFeatureLabels
+            ? [0, 4, 2, 0, 14, 12, 10]
+            : [0, 2, 1, 0, 7, 6, 5]
+          const row = frameOffsets.at(frame)
+          if (row === undefined) {
+            continue
+          }
+          cdsTop = row * rowHeight
           ctx.fillRect(cdsStartPx, cdsTop, cdsWidthPx, cdsHeight)
 
           // Draw lines to connect CDS features with shared mRNA parent
@@ -525,9 +530,14 @@ function drawHover(
         })?.offsetPx ?? 0) - offsetPx
       const cdsStartPx = reversed ? minX - cdsWidthPx : minX
       const frame = getFrame(cds.min, cds.max, strand ?? 1, cds.phase)
-      const frameAdjust =
-        (frame < 0 ? -1 * frame + 5 : frame) * featureLabelSpacer
-      const cdsTop = (frameAdjust - featureLabelSpacer) * rowHeight
+      const frameOffsets = showFeatureLabels
+        ? [0, 4, 2, 0, 14, 12, 10]
+        : [0, 2, 1, 0, 7, 6, 5]
+      const row = frameOffsets.at(frame)
+      if (row === undefined) {
+        continue
+      }
+      const cdsTop = row * rowHeight
       if (counter > 1) {
         // Mid-point for intron line "hat"
         const midPoint: [number, number] = [
@@ -759,8 +769,6 @@ function drawTooltip(
   const displayedRegion = displayedRegions[layoutIndex]
   const { refName, reversed } = displayedRegion
   const rowHeight = apolloRowHeight
-  const cdsHeight = Math.round(0.7 * rowHeight)
-  const featureLabelSpacer = showFeatureLabels ? 2 : 1
   let location = 'Loc: '
   let cds: TranscriptPartCoding | undefined = undefined
   for (const loc of feature.cdsLocations) {
@@ -784,9 +792,14 @@ function drawTooltip(
       regionNumber: layoutIndex,
     })?.offsetPx ?? 0) - offsetPx
   const frame = getFrame(min, max, strand ?? 1, phase)
-  const frameAdjust = (frame < 0 ? -1 * frame + 5 : frame) * featureLabelSpacer
-  const cdsTop =
-    (frameAdjust - featureLabelSpacer) * rowHeight + (rowHeight - cdsHeight) / 2
+  const frameOffsets = showFeatureLabels
+    ? [0, 4, 2, 0, 14, 12, 10]
+    : [0, 2, 1, 0, 7, 6, 5]
+  const row = frameOffsets.at(frame)
+  if (row === undefined) {
+    return
+  }
+  const cdsTop = row * rowHeight
   const cdsWidthPx = (max - min) / bpPerPx
 
   const featureType = `Type: ${cds.type}`

package/src/LinearApolloSixFrameDisplay/glyphs/Glyph.ts

@@ -1,10 +1,10 @@
-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 MousePositionWithFeature } from '../../util'
-import { type LinearApolloSixFrameDisplayMouseEvents } from '../stateModel/mouseEvents'
-import { type LinearApolloSixFrameDisplayRendering } from '../stateModel/rendering'
-import { type CanvasMouseEvent } from '../types'
+import type { MousePositionWithFeature } from '../../util'
+import type { LinearApolloSixFrameDisplayMouseEvents } from '../stateModel/mouseEvents'
+import type { LinearApolloSixFrameDisplayRendering } from '../stateModel/rendering'
+import type { CanvasMouseEvent } from '../types'
 
 export interface Glyph {
   /** draw the feature's primary rendering on the canvas */

package/src/LinearApolloSixFrameDisplay/stateModel/base.ts

@@ -3,10 +3,13 @@
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
 /* eslint-disable @typescript-eslint/no-unsafe-member-access */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
-import { type AnnotationFeature } from '@apollo-annotation/mst'
+import type { AnnotationFeature } from '@apollo-annotation/mst'
 import type PluginManager from '@jbrowse/core/PluginManager'
-import { ConfigurationReference, getConf } from '@jbrowse/core/configuration'
-import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
+import {
+  type AnyConfigurationSchemaType,
+  ConfigurationReference,
+  getConf,
+} from '@jbrowse/core/configuration'
 import { BaseDisplay } from '@jbrowse/core/pluggableElementTypes'
 import {
   type AbstractSessionModel,
@@ -16,14 +19,20 @@ import {
 } from '@jbrowse/core/util'
 import { getParentRenderProps } from '@jbrowse/core/util/tracks'
 // import type LinearGenomeViewPlugin from '@jbrowse/plugin-linear-genome-view'
-import { type LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+import {
+  addDisposer,
+  cast,
+  getRoot,
+  getSnapshot,
+  types,
+} from '@jbrowse/mobx-state-tree'
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 import { autorun } from 'mobx'
-import { addDisposer, cast, getRoot, getSnapshot, types } from 'mobx-state-tree'
 
-import { type ApolloInternetAccountModel } from '../../ApolloInternetAccount/model'
+import type { ApolloInternetAccountModel } from '../../ApolloInternetAccount/model'
 import { FilterFeatures } from '../../components/FilterFeatures'
-import { type ApolloSessionModel, type HoveredFeature } from '../../session'
-import { type ApolloRootModel } from '../../types'
+import type { ApolloSessionModel, HoveredFeature } from '../../session'
+import type { ApolloRootModel } from '../../types'
 import { EditZoomThresholdDialog } from '../../util/displayUtils'
 
 const minDisplayHeight = 20

package/src/LinearApolloSixFrameDisplay/stateModel/index.ts

@@ -1,6 +1,6 @@
 import type PluginManager from '@jbrowse/core/PluginManager'
-import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
-import { type Instance, types } from 'mobx-state-tree'
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration'
+import { type Instance, types } from '@jbrowse/mobx-state-tree'
 
 import { TabularEditorStateModelType } from '../../TabularEditor'
 

package/src/LinearApolloSixFrameDisplay/stateModel/layouts.ts

@@ -1,17 +1,17 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 
-import { type AnnotationFeature } from '@apollo-annotation/mst'
+import type { AnnotationFeature } from '@apollo-annotation/mst'
 import type PluginManager from '@jbrowse/core/PluginManager'
-import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration'
 import {
   type AbstractSessionModel,
   doesIntersect2,
   getFrame,
 } from '@jbrowse/core/util'
+import { addDisposer, isAlive } from '@jbrowse/mobx-state-tree'
 import { autorun, observable } from 'mobx'
-import { addDisposer, isAlive } from 'mobx-state-tree'
 
-import { type ApolloSessionModel } from '../../session'
+import type { ApolloSessionModel } from '../../session'
 import { geneGlyph } from '../glyphs'
 
 import { baseModelFactory } from './base'
@@ -159,15 +159,19 @@ export function layoutsModelFactory(
                   }
                   for (const cdsRow of cdsLocations) {
                     for (const cds of cdsRow) {
-                      let rowNum: number = getFrame(
+                      const frame = getFrame(
                         cds.min,
                         cds.max,
                         strand ?? 1,
                         cds.phase,
                       )
-                      rowNum = self.featureLabelSpacer(
-                        rowNum < 0 ? -1 * rowNum + 5 : rowNum,
-                      )
+                      const frameOffsets = self.showFeatureLabels
+                        ? [0, 5, 3, 1, 15, 13, 11]
+                        : [0, 2, 1, 0, 8, 7, 6]
+                      const rowNum = frameOffsets.at(frame)
+                      if (!rowNum) {
+                        continue
+                      }
                       if (!featureLayout.get(rowNum)) {
                         featureLayout.set(rowNum, [])
                       }

package/src/LinearApolloSixFrameDisplay/stateModel/mouseEvents.ts

@@ -1,15 +1,15 @@
-import { type AnnotationFeature } from '@apollo-annotation/mst'
+import type { AnnotationFeature } from '@apollo-annotation/mst'
 import {
   LocationEndChange,
   LocationStartChange,
 } from '@apollo-annotation/shared'
 import type PluginManager from '@jbrowse/core/PluginManager'
-import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
-import { type MenuItem } from '@jbrowse/core/ui'
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration'
+import type { MenuItem } from '@jbrowse/core/ui'
 import { getFrame } from '@jbrowse/core/util'
+import { type Instance, addDisposer, cast } from '@jbrowse/mobx-state-tree'
 import { autorun } from 'mobx'
-import { type Instance, addDisposer, cast } from 'mobx-state-tree'
-import { type CSSProperties } from 'react'
+import type { CSSProperties } from 'react'
 
 import {
   type Edge,
@@ -19,7 +19,7 @@ import {
   getPropagatedLocationChanges,
   isMousePositionWithFeature,
 } from '../../util'
-import { type CanvasMouseEvent } from '../types'
+import type { CanvasMouseEvent } from '../types'
 
 import { renderingModelFactory } from './rendering'
 
@@ -86,15 +86,16 @@ export function mouseEventsModelIntermediateFactory(
             }
             for (const loc of feature.cdsLocations) {
               for (const cds of loc) {
-                let rowNum: number = getFrame(
+                const frame = getFrame(
                   cds.min,
                   cds.max,
                   feature.strand ?? 1,
                   cds.phase,
                 )
-                rowNum = self.featureLabelSpacer(
-                  rowNum < 0 ? -1 * rowNum + 5 : rowNum,
-                )
+                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 ||

package/src/LinearApolloSixFrameDisplay/stateModel/rendering.ts

@@ -1,17 +1,17 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import type PluginManager from '@jbrowse/core/PluginManager'
-import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration'
 import {
   defaultCodonTable,
   doesIntersect2,
   getFrame,
   revcom,
 } from '@jbrowse/core/util'
+import { type Instance, addDisposer, types } from '@jbrowse/mobx-state-tree'
 import { type Theme, createTheme } from '@mui/material'
 import { autorun } from 'mobx'
-import { type Instance, addDisposer, types } from 'mobx-state-tree'
 
-import { type ApolloSessionModel } from '../../session'
+import type { ApolloSessionModel } from '../../session'
 import { codonColorCode } from '../../util/displayUtils'
 
 import { layoutsModelFactory } from './layouts'

package/src/OntologyManager/OntologyStore/fulltext.test.ts

@@ -6,7 +6,7 @@ import {
   extractWords,
   getWords,
 } from './fulltext'
-import { type OntologyDBNode } from './indexeddb-schema'
+import type { OntologyDBNode } from './indexeddb-schema'
 
 const testNode: OntologyDBNode = {
   id: 'http://purl.obolibrary.org/obo/SO_0000001',

package/src/OntologyManager/OntologyStore/fulltext.ts

@@ -5,16 +5,16 @@
 import { checkAbortSignal } from '@jbrowse/core/util/aborting'
 import jsonpath from 'jsonpath'
 
-import { type TextIndexFieldDefinition } from '..'
+import type { TextIndexFieldDefinition } from '..'
 
 import { stopwords } from './fulltext-stopwords'
-import { type OntologyDBNode } from './indexeddb-schema'
+import type { OntologyDBNode } from './indexeddb-schema'
 import { applyPrefixes } from './prefixes'
 
 // eslint-disable-next-line import/no-duplicates
 import type OntologyStore from '.'
 // eslint-disable-next-line import/no-duplicates
-import { type Transaction } from '.'
+import type { Transaction } from '.'
 
 /** special value of jsonPath that gets the IRI (that is, ID) of the node with the configured prefixes applied */
 export const PREFIXED_ID_PATH = '$PREFIXED_ID'
@@ -28,7 +28,14 @@ function jsonPathQuery(
   if (path === PREFIXED_ID_PATH) {
     return [applyPrefixes(node.id, prefixes)]
   }
-  return jsonpath.query(node, path)
+  let response
+  try {
+    response = jsonpath.query(node, path)
+  } catch {
+    // eslint-disable-next-line unicorn/prefer-structured-clone
+    response = jsonpath.query(JSON.parse(JSON.stringify(node)), path)
+  }
+  return response
 }
 
 function wordsInString(str: string) {

package/src/OntologyManager/OntologyStore/index.test.ts

@@ -1,6 +1,7 @@
 /* eslint-disable @typescript-eslint/no-unsafe-return */
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
 import path from 'node:path'
+import { fileURLToPath } from 'node:url'
 
 import { beforeAll, describe, expect, it, jest } from '@jest/globals'
 
@@ -8,6 +9,8 @@ import { type OntologyClass, isOntologyClass } from '..'
 
 import OntologyStore from '.'
 
+const __dirname = path.dirname(fileURLToPath(import.meta.url))
+
 jest.setTimeout(1_000_000_000)
 
 const prefixes = new Map([

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

@@ -1,13 +1,13 @@
 /** schema types used to strongly-type using the `idb` type system */
-import { type DBSchema } from 'idb/with-async-ittr'
+import type { DBSchema } from 'idb/with-async-ittr'
 
-import {
-  type Edge as OboGraphEdge,
-  type Meta as OboGraphMeta,
-  type Node as OboGraphNode,
+import type {
+  Edge as OboGraphEdge,
+  Meta as OboGraphMeta,
+  Node as OboGraphNode,
 } from './obo-graph-json-schema'
 
-import { type OntologyStoreOptions, type SourceLocation } from '.'
+import type { OntologyStoreOptions, SourceLocation } from '.'
 
 /** metadata about this IndexedDB ontology database */
 export interface Meta {

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

@@ -1,4 +1,5 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
+
 import { openLocation } from '@jbrowse/core/util/io'
 import equal from 'fast-deep-equal/es6'
 import {
@@ -15,7 +16,7 @@ import {
   isOntologyDBEdge,
   isOntologyDBNode,
 } from './indexeddb-schema'
-import { type GraphDocument } from './obo-graph-json-schema'
+import type { GraphDocument } from './obo-graph-json-schema'
 
 import type OntologyStore from '.'