Spreadsheet view refactor to use @mui/x-data-grid component and volatile storage

eslint.config.mjs

@@ -142,6 +142,7 @@ export default tseslint.config(
       '@typescript-eslint/no-unsafe-member-access': 'off',
       '@typescript-eslint/no-unsafe-argument': 'off',
       '@typescript-eslint/no-unsafe-assignment': 'off',
+      '@typescript-eslint/no-deprecated': 'off',
       '@typescript-eslint/restrict-plus-operands': 'off',
       '@typescript-eslint/no-unsafe-call': 'off',
       '@typescript-eslint/no-unsafe-return': 'off',

packages/core/assemblyManager/assembly.ts

@@ -309,6 +309,12 @@ export default function assemblyFactory(
           self.refNameAliases[refName] || self.lowerCaseRefNameAliases[refName]
         )
       },
+      /**
+       * #method
+       */
+      getCanonicalRefNameOrDefault(refName: string) {
+        return this.getCanonicalRefName(refName) || refName
+      },
       /**
        * #method
        */

packages/core/configuration/util.ts

@@ -35,7 +35,7 @@ import {
  *  will be sent to each of the slotNames
  */
 export function readConfObject<CONFMODEL extends AnyConfigurationModel>(
-  confObject: CONFMODEL,
+  confObject: CONFMODEL | Record<string, unknown>,
   slotPath?:
     | ConfigurationSlotName<ConfigurationSchemaForModel<CONFMODEL>>
     | string[],

packages/sv-core/src/BreakendMultiLevelOptionDialog.tsx

@@ -4,7 +4,7 @@ import { Button, DialogActions, DialogContent } from '@mui/material'
 import { getSnapshot } from 'mobx-state-tree'
 import { Dialog } from '@jbrowse/core/ui'
 import { when } from 'mobx'
-import { getSession, Feature } from '@jbrowse/core/util'
+import { Feature, AbstractSessionModel } from '@jbrowse/core/util'
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 
@@ -29,17 +29,17 @@ function stripIds(arr: Track[]) {
 }
 
 const BreakendMultiLevelOptionDialog = observer(function ({
-  model,
+  session,
   handleClose,
   feature,
   assemblyName,
   viewType,
   view,
 }: {
-  model: unknown
+  session: AbstractSessionModel
   handleClose: () => void
   feature: Feature
-  view: LinearGenomeViewModel
+  view?: LinearGenomeViewModel
   assemblyName: string
   viewType: {
     getBreakendCoveringRegions: (arg: {
@@ -63,45 +63,52 @@ const BreakendMultiLevelOptionDialog = observer(function ({
       title="Multi-level breakpoint split view options"
     >
       <DialogContent>
-        <Checkbox2
-          checked={copyTracks}
-          label="Copy tracks into the new view"
-          onChange={event => {
-            setCopyTracks(event.target.checked)
-          }}
-        />
+        <div>Launch multi-level breakpoint split view</div>
+        {view ? (
+          <>
+            <Checkbox2
+              checked={copyTracks}
+              label="Copy tracks into the new view"
+              onChange={event => {
+                setCopyTracks(event.target.checked)
+              }}
+            />
 
-        {copyTracks ? (
-          <Checkbox2
-            checked={mirror}
-            disabled={!copyTracks}
-            label="Mirror the copied tracks (only available if copying tracks and using two level)"
-            onChange={event => {
-              setMirror(event.target.checked)
-            }}
-          />
+            {copyTracks ? (
+              <Checkbox2
+                checked={mirror}
+                disabled={!copyTracks}
+                label="Mirror the copied tracks (only available if copying tracks and using two level)"
+                onChange={event => {
+                  setMirror(event.target.checked)
+                }}
+              />
+            ) : null}
+          </>
         ) : null}
       </DialogContent>
       <DialogActions>
         <Button
           onClick={() => {
             // eslint-disable-next-line @typescript-eslint/no-floating-promises
             ;(async () => {
-              const session = getSession(model)
               try {
-                const asm =
-                  await session.assemblyManager.waitForAssembly(assemblyName)
-                if (!asm) {
+                const { assemblyManager } = session
+                const assembly =
+                  await assemblyManager.waitForAssembly(assemblyName)
+                if (!assembly) {
                   throw new Error(`assembly ${assemblyName} not found`)
                 }
 
                 const { refName, pos, mateRefName, matePos } =
                   viewType.getBreakendCoveringRegions({
                     feature,
-                    assembly: asm,
+                    assembly: assembly,
                   })
 
-                const viewTracks = getSnapshot(view.tracks) as Track[]
+                const viewTracks = view
+                  ? (getSnapshot(view.tracks) as Track[])
+                  : []
                 const breakpointSplitView = session.addView(
                   'BreakpointSplitView',
                   {
@@ -114,7 +121,7 @@ const BreakendMultiLevelOptionDialog = observer(function ({
                       {
                         type: 'LinearGenomeView',
                         hideHeader: true,
-                        tracks: stripIds(getSnapshot(view.tracks)),
+                        tracks: stripIds(viewTracks),
                       },
                       {
                         type: 'LinearGenomeView',
@@ -126,8 +133,10 @@ const BreakendMultiLevelOptionDialog = observer(function ({
                     ],
                   },
                 ) as unknown as { views: LinearGenomeViewModel[] }
-                const r1 = asm.regions!.find(r => r.refName === refName)
-                const r2 = asm.regions!.find(r => r.refName === mateRefName)
+                const r1 = assembly.regions!.find(r => r.refName === refName)
+                const r2 = assembly.regions!.find(
+                  r => r.refName === mateRefName,
+                )
                 if (!r1 || !r2) {
                   throw new Error("can't find regions")
                 }
@@ -172,7 +181,7 @@ const BreakendMultiLevelOptionDialog = observer(function ({
                 breakpointSplitView.views[0]!.centerAt(pos, refName)
               } catch (e) {
                 console.error(e)
-                session.notify(`${e}`)
+                session.notifyError(`${e}`, e)
               }
             })()
             handleClose()

packages/sv-core/src/BreakendSingleLevelOptionDialog.tsx

@@ -4,10 +4,10 @@ import { Button, DialogActions, DialogContent, TextField } from '@mui/material'
 import { getSnapshot } from 'mobx-state-tree'
 import { Dialog } from '@jbrowse/core/ui'
 import {
-  getSession,
   Feature,
   gatherOverlaps,
   useLocalStorage,
+  AbstractSessionModel,
 } from '@jbrowse/core/util'
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
@@ -33,17 +33,17 @@ function stripIds(arr: Track[]) {
 }
 
 const BreakendSingleLevelOptionDialog = observer(function ({
-  model,
+  session,
   handleClose,
   feature,
   assemblyName,
   viewType,
   view,
 }: {
-  model: unknown
+  session: AbstractSessionModel
   handleClose: () => void
   feature: Feature
-  view: LinearGenomeViewModel
+  view?: LinearGenomeViewModel
   assemblyName: string
   viewType: {
     getBreakendCoveringRegions: (arg: {
@@ -70,13 +70,15 @@ const BreakendSingleLevelOptionDialog = observer(function ({
       title="Single-level breakpoint split view options"
     >
       <DialogContent>
-        <Checkbox2
-          checked={copyTracks}
-          label="Copy tracks into the new view"
-          onChange={event => {
-            setCopyTracks(event.target.checked)
-          }}
-        />
+        {view ? (
+          <Checkbox2
+            checked={copyTracks}
+            label="Copy tracks into the new view"
+            onChange={event => {
+              setCopyTracks(event.target.checked)
+            }}
+          />
+        ) : null}
 
         <TextField
           label="Window size (bp)"
@@ -89,17 +91,20 @@ const BreakendSingleLevelOptionDialog = observer(function ({
       <DialogActions>
         <Button
           onClick={() => {
-            const session = getSession(model)
             // eslint-disable-next-line @typescript-eslint/no-floating-promises
             ;(async () => {
               try {
-                const assembly = session.assemblyManager.get(assemblyName)
+                const { assemblyManager } = session
+                const assembly =
+                  await assemblyManager.waitForAssembly(assemblyName)
+                if (!assembly) {
+                  throw new Error(`assembly ${assemblyName} not found`)
+                }
                 const w = +windowSize
                 if (Number.isNaN(w)) {
                   throw new Error('windowSize not a number')
                 }
                 const { refName, pos, mateRefName, matePos } =
-                  // @ts-expect-error
                   viewType.getBreakendCoveringRegions({ feature, assembly })
 
                 const breakpointSplitView = session.addView(
@@ -112,7 +117,9 @@ const BreakendSingleLevelOptionDialog = observer(function ({
                     views: [
                       {
                         type: 'LinearGenomeView',
-                        tracks: stripIds(getSnapshot(view.tracks)),
+                        tracks: view?.tracks
+                          ? stripIds(getSnapshot(view.tracks))
+                          : [],
                       },
                     ],
                   },
@@ -139,7 +146,7 @@ const BreakendSingleLevelOptionDialog = observer(function ({
                 )
               } catch (e) {
                 console.error(e)
-                session.notify(`${e}`)
+                session.notifyError(`${e}`, e)
               }
             })()
             handleClose()

plugins/alignments/src/AlignmentsFeatureDetail/util.ts

@@ -22,6 +22,6 @@ export async function navToLoc(locString: string, model: IAnyStateTreeNode) {
     }
   } catch (e) {
     console.error(e)
-    session.notify(`${e}`)
+    session.notifyError(`${e}`, e)
   }
 }

plugins/alignments/src/LinearPileupDisplay/SharedLinearPileupDisplayMixin.ts

@@ -421,7 +421,7 @@ export function SharedLinearPileupDisplayMixin(
                 }
               } catch (e) {
                 console.error(e)
-                session.notify(`${e}`)
+                session.notifyError(`${e}`, e)
               }
             },
 
@@ -455,7 +455,7 @@ export function SharedLinearPileupDisplayMixin(
                 }
               } catch (e) {
                 console.error(e)
-                session.notify(`${e}`)
+                session.notifyError(`${e}`, e)
               }
             },
           }

plugins/breakpoint-split-view/src/BreakpointSplitView/BreakpointSplitView.ts

@@ -1,7 +1,6 @@
-import { getSession, Feature, Region } from '@jbrowse/core/util'
+import { Feature, AbstractSessionModel } from '@jbrowse/core/util'
 import ViewType from '@jbrowse/core/pluggableElementTypes/ViewType'
 import { parseBreakend } from '@gmod/vcf'
-import { IStateTreeNode } from 'mobx-state-tree'
 import { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 
 export default class BreakpointSplitViewType extends ViewType {
@@ -52,22 +51,23 @@ export default class BreakpointSplitViewType extends ViewType {
     }
   }
 
-  singleLevelSnapshotFromBreakendFeature(
-    feature: Feature,
-    view: { displayedRegions: Region[] } & IStateTreeNode,
-  ) {
-    const session = getSession(view)
+  async singleLevelSnapshotFromBreakendFeature({
+    feature,
+    assemblyName,
+    session,
+  }: {
+    feature: Feature
+    assemblyName: string
+    session: AbstractSessionModel
+  }) {
     const bpPerPx = 10
-    const { assemblyName } = view.displayedRegions[0]!
 
     const { assemblyManager } = session
-    const assembly = assemblyManager.get(assemblyName)
-    if (!assembly) {
+    const assembly = await assemblyManager.waitForAssembly(assemblyName)
+    if (!assembly?.regions) {
       throw new Error(`assembly ${assemblyName} not found`)
     }
-    if (!assembly.regions) {
-      throw new Error(`assembly ${assemblyName} regions not loaded`)
-    }
+
     const {
       refName,
       pos: startPos,
@@ -103,23 +103,22 @@ export default class BreakpointSplitViewType extends ViewType {
       featureData: undefined as unknown,
     }
   }
-
-  snapshotFromBreakendFeature(
-    feature: Feature,
-    view: { displayedRegions: Region[] } & IStateTreeNode,
-  ) {
-    const session = getSession(view)
+  async snapshotFromBreakendFeature({
+    feature,
+    assemblyName,
+    session,
+  }: {
+    feature: Feature
+    assemblyName: string
+    session: AbstractSessionModel
+  }) {
     const bpPerPx = 10
-    const { assemblyName } = view.displayedRegions[0]!
-
     const { assemblyManager } = session
-    const assembly = assemblyManager.get(assemblyName)
-    if (!assembly) {
+    const assembly = await assemblyManager.waitForAssembly(assemblyName)
+    if (!assembly?.regions) {
       throw new Error(`assembly ${assemblyName} not found`)
     }
-    if (!assembly.regions) {
-      throw new Error(`assembly ${assemblyName} regions not loaded`)
-    }
+
     const {
       refName,
       pos: startPos,