Squash updates

Remove clone. It seems to be unneeded, even though it will mutate the original object, this doesn't seem like it should matter

Another optimization to the track selector

Use structuredClone

Misc lint fixes

Misc

packages/app-core/src/JBrowseConfig/index.ts

@@ -36,9 +36,11 @@ import { types } from 'mobx-state-tree'
 export function JBrowseConfigF({
  pluginManager,
  assemblyConfigSchema,
+ adminMode,
 }: {
  pluginManager: PluginManager
  assemblyConfigSchema: AnyConfigurationSchemaType
+ adminMode: boolean
 }) {
  return types.model('JBrowseConfig', {
  configuration: ConfigurationSchema('Root', {
@@ -121,7 +123,11 @@ export function JBrowseConfigF({
  * track configuration is an array of track config schemas. multiple
  * instances of a track can exist that use the same configuration
  */
- tracks: types.array(pluginManager.pluggableConfigSchemaType('track')),
+ tracks:
+ // @ts-expect-error
+ adminMode || globalThis.disableFrozenTracks
+ ? types.array(pluginManager.pluggableConfigSchemaType('track'))
+ : types.frozen([] as { trackId: string; [key: string]: unknown }[]),
  /**
  * #slot
  * configuration for internet accounts, see InternetAccounts

packages/app-core/src/JBrowseModel/index.ts

@@ -24,13 +24,15 @@ import { JBrowseConfigF } from '../JBrowseConfig'
 
  */
 export function JBrowseModelF({
+ adminMode,
  pluginManager,
  assemblyConfigSchema,
 }: {
+ adminMode: boolean
  pluginManager: PluginManager
  assemblyConfigSchema: BaseAssemblyConfigSchema
 }) {
- return JBrowseConfigF({ pluginManager, assemblyConfigSchema })
+ return JBrowseConfigF({ pluginManager, assemblyConfigSchema, adminMode })
  .views(self => ({
  /**
  * #getter
@@ -81,13 +83,17 @@ export function JBrowseModelF({
  /**
  * #action
  */
- addTrackConf(trackConf: AnyConfigurationModel) {
+ addTrackConf(trackConf: { trackId: string; type: string }) {
  const { type } = trackConf
  if (!type) {
  throw new Error(`unknown track type ${type}`)
  }
- const length = self.tracks.push(trackConf)
- return self.tracks[length - 1]
+ if (adminMode) {
+ self.tracks.push(trackConf)
+ } else {
+ self.tracks = [...self.tracks, trackConf]
+ }
+ return self.tracks.at(-1)
  },
  /**
  * #action
@@ -111,8 +117,13 @@ export function JBrowseModelF({
  * #action
  */
  deleteTrackConf(trackConf: AnyConfigurationModel) {
- const elt = self.tracks.find(t => t.trackId === trackConf.trackId)
- return self.tracks.remove(elt)
+ if (adminMode) {
+ const elt = self.tracks.find(t => t.trackId === trackConf.trackId)
+ // @ts-expect-error
+ return self.tracks.remove(elt)
+ } else {
+ return self.tracks.filter(f => f.trackId !== trackConf.trackId)
+ }
  },
  /**
  * #action

packages/core/configuration/configurationSchema.ts

@@ -6,13 +6,17 @@ import {
  getSnapshot,
  IAnyType,
  SnapshotOut,
+ getEnv,
+ getRoot,
+ resolveIdentifier,
 } from 'mobx-state-tree'
 
 import { ElementId } from '../util/types/mst'
 
 import ConfigSlot, { ConfigSlotDefinition } from './configurationSlot'
 import { isConfigurationSchemaType } from './util'
 import { AnyConfigurationSchemaType } from './types'
+import { getContainingTrack, getSession } from '../util'
 
 export type {
  AnyConfigurationSchemaType,
@@ -276,9 +280,55 @@ export function ConfigurationSchema<
  return schemaType
 }
 
+export function TrackConfigurationReference(schemaType: IAnyType) {
+ const trackRef = types.reference(schemaType, {
+ get(id, parent) {
+ let ret = getSession(parent).tracksById[id]
+ if (!ret) {
+ // @ts-expect-error
+ ret = resolveIdentifier(schemaType, getRoot(parent), id)
+ }
+ if (!ret) {
+ throw new Error(`${id} not found`)
+ }
+ return isStateTreeNode(ret) ? ret : schemaType.create(ret, getEnv(parent))
+ },
+ set(value) {
+ return value.trackId
+ },
+ })
+ return types.union(trackRef, schemaType)
+}
+
+export function DisplayConfigurationReference(schemaType: IAnyType) {
+ const displayRef = types.reference(schemaType, {
+ get(id, parent) {
+ const track = getContainingTrack(parent)
+ let ret = track.configuration.displays.find(u => u.displayId === id)
+ if (!ret) {
+ // @ts-expect-error
+ ret = resolveIdentifier(schemaType, getRoot(parent), id)
+ }
+ if (!ret) {
+ throw new Error(`${id} not found`)
+ }
+ return ret
+ },
+ set(value) {
+ return value.displayId
+ },
+ })
+ return types.union(displayRef, schemaType)
+}
+
 export function ConfigurationReference<
  SCHEMATYPE extends AnyConfigurationSchemaType,
 >(schemaType: SCHEMATYPE) {
+ if (schemaType.name.endsWith('TrackConfigurationSchema')) {
+ return TrackConfigurationReference(schemaType)
+ } else if (schemaType.name.endsWith('DisplayConfigurationSchema')) {
+ return DisplayConfigurationReference(schemaType)
+ }
  // we cast this to SCHEMATYPE, because the reference *should* behave just
  // like the object it points to. It won't be undefined (this is a
  // `reference`, not a `safeReference`)

packages/core/util/tracks.ts

@@ -1,4 +1,13 @@
-import { getParent, isRoot, IAnyStateTreeNode } from 'mobx-state-tree'
+import {
+ getParent,
+ getRoot,
+ isRoot,
+ resolveIdentifier,
+ types,
+ IAnyStateTreeNode,
+ Instance,
+ IAnyType,
+} from 'mobx-state-tree'
 import { getSession, objectHash, getEnv } from './index'
 import { PreFileLocation, FileLocation } from './types'
 import { readConfObject, AnyConfigurationModel } from '../configuration'
@@ -268,3 +277,95 @@ export function getTrackName(
  }
  return trackName
 }
+
+type MSTArray<T extends IAnyType> = Instance<ReturnType<typeof types.array<T>>>
+
+interface MinimalTrack extends IAnyType {
+ configuration: { trackId: string }
+}
+
+interface GenericView {
+ type: string
+ tracks: MSTArray<MinimalTrack>
+}
+
+export function showTrackGeneric(
+ self: GenericView,
+ trackId: string,
+ initialSnapshot = {},
+ displayInitialSnapshot = {},
+) {
+ const { pluginManager } = getEnv(self)
+ const session = getSession(self)
+ let conf = session.tracks.find(t => t.trackId === trackId)
+ if (!conf) {
+ const schema = pluginManager.pluggableConfigSchemaType('track')
+ conf = resolveIdentifier(schema, getRoot(self), trackId)
+ }
+ if (!conf) {
+ throw new Error(`Could not resolve identifier "${trackId}"`)
+ }
+ const trackType = pluginManager.getTrackType(conf.type)
+ if (!trackType) {
+ throw new Error(`Unknown track type ${conf.type}`)
+ }
+ const viewType = pluginManager.getViewType(self.type)!
+ const supportedDisplays = new Set(viewType.displayTypes.map(d => d.name))
+
+ const { displays = [] } = conf
+ const displayTypes = new Set()
+
+ displays.forEach((d: any) => d && displayTypes.add(d.type))
+ trackType.displayTypes.forEach(displayType => {
+ if (!displayTypes.has(displayType.name)) {
+ displays.push({
+ displayId: `${trackId}-${displayType.name}`,
+ type: displayType.name,
+ })
+ }
+ })
+
+ const displayConf = displays?.find((d: AnyConfigurationModel) =>
+ supportedDisplays.has(d.type),
+ )
+ if (!displayConf) {
+ throw new Error(
+ `Could not find a compatible display for view type ${self.type}`,
+ )
+ }
+
+ const found = self.tracks.find(t => t.configuration.trackId === trackId)
+ if (!found) {
+ const track = trackType.stateModel.create({
+ ...initialSnapshot,
+ type: conf.type,
+ configuration: conf,
+ displays: [
+ {
+ type: displayConf.type,
+ configuration: displayConf,
+ ...displayInitialSnapshot,
+ },
+ ],
+ })
+ self.tracks.push(track)
+ return track
+ }
+ return found
+}
+
+export function hideTrackGeneric(self: GenericView, trackId: string) {
+ const t = self.tracks.find(t => t.configuration.trackId === trackId)
+ if (t) {
+ self.tracks.remove(t)
+ return 1
+ }
+ return 0
+}
+
+export function toggleTrackGeneric(self: GenericView, trackId: string) {
+ const hiddenCount = hideTrackGeneric(self, trackId)
+ if (!hiddenCount) {
+ showTrackGeneric(self, trackId)
+ }
+}

packages/core/util/types/index.ts

@@ -81,6 +81,7 @@ export type DialogComponentType =
 
 /** minimum interface that all session state models must implement */
 export interface AbstractSessionModel extends AbstractViewContainer {
+ tracksById: Record<string, AnyConfigurationModel>
  jbrowse: IAnyStateTreeNode
  drawerPosition?: string
  configuration: AnyConfigurationModel
@@ -295,9 +296,11 @@ export function isViewModel(thing: unknown): thing is AbstractViewModel {
  )
 }
 
+type Display = { displayId: string } & AnyConfigurationModel
+
 export interface AbstractTrackModel {
  displays: AbstractDisplayModel[]
- configuration: AnyConfigurationModel
+ configuration: AnyConfigurationModel & { displays: Display[] }
 }
 
 export function isTrackModel(thing: unknown): thing is AbstractTrackModel {

packages/product-core/src/Session/Tracks.ts

@@ -28,6 +28,13 @@ export function TracksManagerSessionMixin(pluginManager: PluginManager) {
  get tracks(): AnyConfigurationModel[] {
  return self.jbrowse.tracks
  },
+
+ /**
+ * #getter
+ */
+ get tracksById(): Record<string, AnyConfigurationModel> {
+ return Object.fromEntries(this.tracks.map(t => [t.trackId, t]))
+ },
  }))
  .actions(self => ({
  /**

packages/product-core/src/ui/AboutDialog.tsx

@@ -1,30 +1,36 @@
 import React from 'react'
 import { AnyConfigurationModel } from '@jbrowse/core/configuration'
 import Dialog from '@jbrowse/core/ui/Dialog'
-import { getSession, getEnv } from '@jbrowse/core/util'
+import { getEnv, AbstractSessionModel } from '@jbrowse/core/util'
 import { getTrackName } from '@jbrowse/core/util/tracks'
+
+// locals
 import AboutContents from './AboutDialogContents'
 
 export function AboutDialog({
  config,
+ session,
  handleClose,
 }: {
  config: AnyConfigurationModel
+ session: AbstractSessionModel
  handleClose: () => void
 }) {
- const session = getSession(config)
  const trackName = getTrackName(config, session)
  const { pluginManager } = getEnv(session)
 
  const AboutComponent = pluginManager.evaluateExtensionPoint(
  'Core-replaceAbout',
  AboutContents,
  { session, config },
- ) as React.FC<any>
+ ) as React.FC<{
+ config: AnyConfigurationModel
+ session: AbstractSessionModel
+ }>
 
  return (
  <Dialog open onClose={handleClose} title={trackName} maxWidth="xl">
- <AboutComponent config={config} />
+ <AboutComponent config={config} session={session} />
  </Dialog>
  )
 }

packages/product-core/src/ui/AboutDialogContents.tsx

@@ -9,13 +9,14 @@ import {
  readConfObject,
  AnyConfigurationModel,
 } from '@jbrowse/core/configuration'
-import { getSession, getEnv } from '@jbrowse/core/util'
+import { getEnv, AbstractSessionModel } from '@jbrowse/core/util'
 import {
  BaseCard,
  Attributes,
 } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail'
 import FileInfoPanel from './FileInfoPanel'
 import RefNameInfoDialog from './RefNameInfoDialog'
+import { isStateTreeNode } from 'mobx-state-tree'
 
 const useStyles = makeStyles()({
  content: {
@@ -39,12 +40,13 @@ function removeAttr(obj: Record<string, unknown>, attr: string) {
 
 const AboutDialogContents = observer(function ({
  config,
+ session,
 }: {
  config: AnyConfigurationModel
+ session: AbstractSessionModel
 }) {
  const [copied, setCopied] = useState(false)
- const conf = readConfObject(config)
- const session = getSession(config)
+ const conf = isStateTreeNode(config) ? readConfObject(config) : config
  const { classes } = useStyles()
  const [showRefNames, setShowRefNames] = useState(false)
 
@@ -112,9 +114,10 @@ const AboutDialogContents = observer(function ({
  <ExtraPanel.Component config={config} />
  </BaseCard>
  ) : null}
- <FileInfoPanel config={config} />
+ <FileInfoPanel config={config} session={session} />
  {showRefNames ? (
  <RefNameInfoDialog
+ session={session}
  config={config}
  onClose={() => {
  setShowRefNames(false)