Create new config schema for ReferenceSequenceTrack based on the base…

… track, but without assemblyNames, etc. (#1434)

* Create refSeq track config

* Add comment about duplication

* Fix comment

* Fix getting track name

packages/core/util/tracks.ts

@@ -11,7 +11,7 @@ export function getTrackAssemblyNames(
 ) {
   const trackConf = track.configuration
   const trackAssemblyNames = readConfObject(trackConf, 'assemblyNames')
-  if (trackAssemblyNames[0] === 'assemblyName') {
+  if (!trackAssemblyNames) {
     // Check if it's an assembly sequence track
     // eslint-disable-next-line @typescript-eslint/no-explicit-any
     const parent = getParent<any>(track.configuration)

plugins/sequence/src/index.ts

@@ -1,9 +1,5 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
-import {
-  createBaseTrackConfig,
-  createBaseTrackModel,
-} from '@jbrowse/core/pluggableElementTypes/models'
+import { createBaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models'
 import ServerSideRendererType from '@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType'
 import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType'
 import Plugin from '@jbrowse/core/Plugin'
@@ -33,6 +29,7 @@ import {
   AdapterClass as TwoBitAdapterClass,
   configSchema as twoBitAdapterConfigSchema,
 } from './TwoBitAdapter'
+import { createReferenceSeqTrackConfig } from './referenceSeqTrackConfig'
 
 export default class SequencePlugin extends Plugin {
   name = 'SequencePlugin'
@@ -75,14 +72,8 @@ export default class SequencePlugin extends Plugin {
     )
 
     pluginManager.addTrackType(() => {
-      const configSchema = ConfigurationSchema(
-        'ReferenceSequenceTrack',
-        {},
-        {
-          baseConfiguration: createBaseTrackConfig(pluginManager),
-          explicitIdentifier: 'trackId',
-        },
-      )
+      const configSchema = createReferenceSeqTrackConfig(pluginManager)
+
       return new TrackType({
         name: 'ReferenceSequenceTrack',
         configSchema,

plugins/sequence/src/referenceSeqTrackConfig.ts

@@ -0,0 +1,63 @@
+/* eslint-disable @typescript-eslint/no-explicit-any */
+import { types } from 'mobx-state-tree'
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
+import PluginManager from '@jbrowse/core/PluginManager'
+
+/*
+Note: this is primarily a copy of createBaseTrackConfig, except with a subset
+of the config slots, to avoid including fields that don't make sense for the
+ReferenceSequenceTrack
+*/
+export function createReferenceSeqTrackConfig(pluginManager: PluginManager) {
+  return ConfigurationSchema(
+    'ReferenceSequenceTrack',
+    {
+      adapter: pluginManager.pluggableConfigSchemaType('adapter'),
+      displays: types.array(pluginManager.pluggableConfigSchemaType('display')),
+      metadata: {
+        type: 'frozen',
+        description: 'anything to add about this track',
+        defaultValue: {},
+      },
+    },
+    {
+      preProcessSnapshot: s => {
+        const snap = JSON.parse(JSON.stringify(s))
+        const displayTypes = new Set()
+        const { displays = [] } = snap
+        if (snap.trackId !== 'placeholderId') {
+          // Gets the displays on the track snapshot and the possible displays
+          // from the track type and adds any missing possible displays to the
+          // snapshot
+          displays.forEach((d: any) => d && displayTypes.add(d.type))
+          const trackType = pluginManager.getTrackType(snap.type)
+          trackType.displayTypes.forEach(displayType => {
+            if (!displayTypes.has(displayType.name)) {
+              displays.push({
+                displayId: `${snap.trackId}-${displayType.name}`,
+                type: displayType.name,
+              })
+            }
+          })
+        }
+        return { ...snap, displays }
+      },
+      explicitIdentifier: 'trackId',
+      explicitlyTyped: true,
+      actions: (self: any) => ({
+        addDisplayConf(displayConf: { type: string; displayId: string }) {
+          const { type } = displayConf
+          if (!type) throw new Error(`unknown display type ${type}`)
+          const display = self.displays.find(
+            (d: any) => d && d.displayId === displayConf.displayId,
+          )
+          if (display) {
+            return display
+          }
+          const length = self.displays.push(displayConf)
+          return self.displays[length - 1]
+        },
+      }),
+    },
+  )
+}