More notifyError

eslint.config.mjs

@@ -139,6 +139,7 @@ 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/pluggableElementTypes/renderers/RpcRenderedSvgGroup.tsx

@@ -69,7 +69,7 @@ const OldHydrate = observer(function OldHydrate(props: Props) {
     function doHydrate() {
       if (domNode && html) {
         if (domNode.innerHTML) {
-          // eslint-disable-next-line @typescript-eslint/no-deprecated
+           
           unmountComponentAtNode(domNode)
         }
 
@@ -81,15 +81,15 @@ const OldHydrate = observer(function OldHydrate(props: Props) {
         // hydration for when we have some free time. helps keep the
         // framerate up.
         rIC(() => {
-          // eslint-disable-next-line @typescript-eslint/no-deprecated
+           
           hydrate(<RenderingComponent {...props} />, domNode)
         })
       }
     }
     doHydrate()
     return () => {
       if (domNode) {
-        // eslint-disable-next-line @typescript-eslint/no-deprecated
+         
         unmountComponentAtNode(domNode)
       }
     }

packages/core/pluggableElementTypes/renderers/ServerSideRenderedContent.tsx

@@ -82,12 +82,12 @@ const OldHydrate = observer(function ({
     const domNode = ref.current
     function doHydrate() {
       if (domNode) {
-        // eslint-disable-next-line @typescript-eslint/no-deprecated
+         
         unmountComponentAtNode(domNode)
         domNode.innerHTML = html
 
         rIC(() => {
-          // eslint-disable-next-line @typescript-eslint/no-deprecated
+           
           hydrate(
             <ThemeProvider theme={jbrowseTheme}>
               <RenderingComponent {...rest} />
@@ -102,7 +102,7 @@ const OldHydrate = observer(function ({
 
     return () => {
       if (domNode) {
-        // eslint-disable-next-line @typescript-eslint/no-deprecated
+         
         unmountComponentAtNode(domNode)
       }
     }

packages/core/util/index.ts

@@ -1458,7 +1458,7 @@ export function renderToStaticMarkup(
     if (createRootFn) {
       createRootFn(div).render(node)
     } else {
-      // eslint-disable-next-line @typescript-eslint/no-deprecated
+       
       render(node, div)
     }
   })

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

@@ -395,7 +395,7 @@ export function SharedLinearPileupDisplayMixin(
                 }
               } catch (e) {
                 console.error(e)
-                session.notify(`${e}`)
+                session.notifyError(`${e}`, e)
               }
             },
 
@@ -429,7 +429,7 @@ export function SharedLinearPileupDisplayMixin(
                 }
               } catch (e) {
                 console.error(e)
-                session.notify(`${e}`)
+                session.notifyError(`${e}`, e)
               }
             },
           }

plugins/circular-view/src/CircularView/models/model.ts

@@ -363,6 +363,9 @@ function stateModelFactory(pluginManager: PluginManager) {
     }))
 
     .actions(self => ({
+      clearTracks() {
+        self.tracks = cast([])
+      },
       /**
        * #action
        */

plugins/linear-genome-view/src/LinearGenomeView/components/RefNameAutocomplete/AutocompleteTextField.tsx

@@ -23,7 +23,7 @@ export default function AutocompleteTextField({
   setInputValue: (arg: string) => void
   setCurrentSearch: (arg: string) => void
 }) {
-  // eslint-disable-next-line @typescript-eslint/no-deprecated
+   
   const { helperText, InputProps = {} } = TextFieldProps
   return (
     <TextField

plugins/linear-genome-view/src/LinearGenomeView/components/SearchResultsTable.tsx

@@ -64,7 +64,7 @@ export default function SearchResultsTable({
       }
     } catch (e) {
       console.warn(e)
-      session.notify(`${e}`, 'warning')
+      session.notifyError(`${e}`, e)
     }
   }
   return (

plugins/spreadsheet-view/src/SpreadsheetView/components/util.ts

@@ -1,9 +1,4 @@
-import {
-  AbstractSessionModel,
-  FileLocation,
-  getSession,
-} from '@jbrowse/core/util'
-import { getParent } from 'mobx-state-tree'
+import { AbstractSessionModel, FileLocation } from '@jbrowse/core/util'
 import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 
 type LGV = LinearGenomeViewModel

plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/BedpeImport.ts

@@ -1,4 +1,5 @@
 import { parseStrand } from './util'
+import type { Buffer } from 'buffer'
 
 export function parseBedPEBuffer(buffer: Buffer) {
   const data = new TextDecoder('utf8', { fatal: true }).decode(buffer)

plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/components/BreakendMultiLevelOptionDialog.tsx

@@ -0,0 +1,2 @@
+// re-exported for react lazy
+export { BreakendMultiLevelOptionDialog as default } from '@jbrowse/sv-core'

plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/components/BreakendSingleLevelOptionDialog.tsx

@@ -0,0 +1,2 @@
+// re-exported for react lazy
+export { BreakendSingleLevelOptionDialog as default } from '@jbrowse/sv-core'