Fix opening temporaryAssemblies sequence tracks (#5393)

Author: cmdcolin

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

@@ -31,19 +31,30 @@ export function TracksManagerSessionMixin(pluginManager: PluginManager) {
         return self.jbrowse.tracks
       },
 
+      /**
+       * #getter
+       * Base assemblies from jbrowse config. Child sessions can override
+       * to include additional assemblies (e.g. sessionAssemblies).
+       */
+      get assemblies(): { sequence: { trackId: string } }[] {
+        return self.jbrowse.assemblies
+      },
+
       /**
        * #getter
        */
       get tracksById(): Record<string, AnyConfigurationModel> {
+        const temporaryAssemblies =
+          'temporaryAssemblies' in self
+            ? (self.temporaryAssemblies as { sequence: { trackId: string } }[])
+            : []
+
         return Object.fromEntries([
           ...this.tracks.map(t => [t.trackId, t]),
           // Include assembly sequence tracks so they can be resolved by trackId
-          ...self.jbrowse.assemblies.map(
-            (a: { sequence: { trackId: string } }) => [
-              a.sequence.trackId,
-              a.sequence,
-            ],
-          ),
+          ...this.assemblies.map(a => [a.sequence.trackId, a.sequence]),
+          // Include temporary assembly sequence tracks
+          ...temporaryAssemblies.map(a => [a.sequence.trackId, a.sequence]),
         ])
       },
     }))

packages/web-core/src/BaseWebSession/index.ts

@@ -126,15 +126,6 @@ export function BaseWebSession({
       task: undefined,
     }))
     .views(self => ({
-      /**
-       * #getter
-       */
-      get tracksById(): Record<string, AnyConfigurationModel> {
-        return Object.fromEntries([
-          ...this.tracks.map(t => [t.trackId, t]),
-          ...this.assemblies.map(a => [a.sequence.trackId, a.sequence]),
-        ])
-      },
       /**
        * #getter
        */

products/jbrowse-web/src/tests/TemporaryAssembly.test.tsx

@@ -0,0 +1,68 @@
+import { fireEvent, waitFor } from '@testing-library/react'
+
+import { createView, doBeforeEach, hts, setup } from './util.tsx'
+
+setup()
+
+beforeEach(() => {
+  doBeforeEach()
+})
+
+const delay = { timeout: 10000 }
+const opts = [{}, delay]
+
+test('add temporary assembly and toggle reference sequence track', async () => {
+  const { session, view, findByTestId, findAllByText } = await createView()
+
+  // Wait for initial view to load
+  await findAllByText('ctgA', ...opts)
+
+  const testAssemblyName = 'testProtein'
+  const refSeqTrackId = `${testAssemblyName}-ReferenceSequenceTrack`
+
+  // Add a temporary assembly programmatically
+  session.addTemporaryAssembly?.({
+    name: testAssemblyName,
+    sequence: {
+      type: 'ReferenceSequenceTrack',
+      trackId: refSeqTrackId,
+      adapter: {
+        type: 'FromConfigSequenceAdapter',
+        features: [
+          {
+            refName: testAssemblyName,
+            uniqueId: 'test-seq-1',
+            start: 0,
+            end: 100,
+            seq: 'MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSH',
+          },
+        ],
+      },
+    },
+  })
+
+  // Verify the assembly was added
+  expect(session.temporaryAssemblies?.length).toBeGreaterThan(0)
+
+  // Clear the current view and navigate to the new assembly
+  view.clearView()
+
+  // Try to navigate to the new assembly
+  await view.navToLocString(testAssemblyName, testAssemblyName)
+
+  // Now try to toggle the reference sequence track via UI
+  // The track selector should show the reference sequence track for this assembly
+  const trackEntry = await findByTestId(hts(refSeqTrackId), ...opts)
+  fireEvent.click(trackEntry)
+
+  // Wait for the track to be added
+  await waitFor(
+    () => {
+      expect(view.tracks.length).toBe(1)
+    },
+    { timeout: 10000 },
+  )
+
+  // Verify the track was added successfully
+  expect(view.tracks[0]?.configuration.trackId).toBe(refSeqTrackId)
+}, 60000)