From 075ed055ffcf24f48fc2e30c3599144bc6c06a75 Mon Sep 17 00:00:00 2001
From: Colin <colin.diesh@gmail.com>
Date: Tue, 24 Sep 2024 10:22:18 -0400
Subject: [PATCH] More notifyError

---
 eslint.config.mjs                             |  1 +
 .../renderers/RpcRenderedSvgGroup.tsx         |  6 +-
 .../renderers/ServerSideRenderedContent.tsx   |  6 +-
 packages/core/util/index.ts                   |  2 +-
 .../src/BreakendMultiLevelOptionDialog.tsx    | 69 +++++++-------
 .../src/BreakendSingleLevelOptionDialog.tsx   | 39 ++++----
 .../src/AlignmentsFeatureDetail/util.ts       |  2 +-
 .../SharedLinearPileupDisplayMixin.ts         |  4 +-
 .../src/CircularView/models/model.ts          |  3 +
 .../AutocompleteTextField.tsx                 |  2 +-
 .../components/SearchResultsTable.tsx         |  2 +-
 .../src/SpreadsheetView/components/util.ts    |  7 +-
 .../importAdapters/BedpeImport.ts             |  1 +
 .../BreakendMultiLevelOptionDialog.tsx        |  2 +
 .../BreakendSingleLevelOptionDialog.tsx       |  2 +
 .../importAdapters/components/FeatureMenu.tsx | 63 ++++++-------
 .../importAdapters/components/LocString.tsx   |  2 +-
 .../SpreadsheetView/models/ImportWizard.ts    |  2 +-
 .../SpreadsheetView/models/SpreadsheetView.ts |  2 +-
 .../SvInspectorView/models/SvInspectorView.ts | 89 ++++++++-----------
 .../LaunchBreakendPanel.tsx                   |  6 +-
 .../saved-sessions/jbrowse_analytics.js       |  2 +-
 .../jbrowse-desktop/src/indexJobsModel.ts     | 15 +---
 products/jbrowse-web/src/SessionLoader.ts     |  2 +-
 .../jbrowse-web/src/components/JBrowse.tsx    |  3 +-
 .../src/tests/SVInspector.test.tsx            |  3 -
 26 files changed, 169 insertions(+), 168 deletions(-)
 create mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/components/BreakendMultiLevelOptionDialog.tsx
 create mode 100644 plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/components/BreakendSingleLevelOptionDialog.tsx

diff --git a/eslint.config.mjs b/eslint.config.mjs
index 6447d40db5..2ee51af394 100644
--- a/eslint.config.mjs
+++ b/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',
diff --git a/packages/core/pluggableElementTypes/renderers/RpcRenderedSvgGroup.tsx b/packages/core/pluggableElementTypes/renderers/RpcRenderedSvgGroup.tsx
index a154263186..0886d31ff2 100644
--- a/packages/core/pluggableElementTypes/renderers/RpcRenderedSvgGroup.tsx
+++ b/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)
         }
 
@@ -81,7 +81,7 @@ 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)
         })
       }
@@ -89,7 +89,7 @@ const OldHydrate = observer(function OldHydrate(props: Props) {
     doHydrate()
     return () => {
       if (domNode) {
-        // eslint-disable-next-line @typescript-eslint/no-deprecated
+         
         unmountComponentAtNode(domNode)
       }
     }
diff --git a/packages/core/pluggableElementTypes/renderers/ServerSideRenderedContent.tsx b/packages/core/pluggableElementTypes/renderers/ServerSideRenderedContent.tsx
index 8566a33769..51bb7d1d06 100644
--- a/packages/core/pluggableElementTypes/renderers/ServerSideRenderedContent.tsx
+++ b/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)
       }
     }
diff --git a/packages/core/util/index.ts b/packages/core/util/index.ts
index 0046a00143..0f0ec9921b 100644
--- a/packages/core/util/index.ts
+++ b/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)
     }
   })
diff --git a/packages/sv-core/src/BreakendMultiLevelOptionDialog.tsx b/packages/sv-core/src/BreakendMultiLevelOptionDialog.tsx
index 75412d5f5c..edaac4b5e0 100644
--- a/packages/sv-core/src/BreakendMultiLevelOptionDialog.tsx
+++ b/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: {
@@ -63,23 +63,28 @@ 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>
@@ -87,21 +92,23 @@ const BreakendMultiLevelOptionDialog = observer(function ({
           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()
diff --git a/packages/sv-core/src/BreakendSingleLevelOptionDialog.tsx b/packages/sv-core/src/BreakendSingleLevelOptionDialog.tsx
index a1a17e2310..18dbbd6785 100644
--- a/packages/sv-core/src/BreakendSingleLevelOptionDialog.tsx
+++ b/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()
diff --git a/plugins/alignments/src/AlignmentsFeatureDetail/util.ts b/plugins/alignments/src/AlignmentsFeatureDetail/util.ts
index ec69541940..495784eacb 100644
--- a/plugins/alignments/src/AlignmentsFeatureDetail/util.ts
+++ b/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)
   }
 }
diff --git a/plugins/alignments/src/LinearPileupDisplay/SharedLinearPileupDisplayMixin.ts b/plugins/alignments/src/LinearPileupDisplay/SharedLinearPileupDisplayMixin.ts
index 7eb1631e4c..e3cbf53a31 100644
--- a/plugins/alignments/src/LinearPileupDisplay/SharedLinearPileupDisplayMixin.ts
+++ b/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)
               }
             },
           }
diff --git a/plugins/circular-view/src/CircularView/models/model.ts b/plugins/circular-view/src/CircularView/models/model.ts
index 686a12d982..b0cc9598b5 100644
--- a/plugins/circular-view/src/CircularView/models/model.ts
+++ b/plugins/circular-view/src/CircularView/models/model.ts
@@ -363,6 +363,9 @@ function stateModelFactory(pluginManager: PluginManager) {
     }))
 
     .actions(self => ({
+      clearTracks() {
+        self.tracks = cast([])
+      },
       /**
        * #action
        */
diff --git a/plugins/linear-genome-view/src/LinearGenomeView/components/RefNameAutocomplete/AutocompleteTextField.tsx b/plugins/linear-genome-view/src/LinearGenomeView/components/RefNameAutocomplete/AutocompleteTextField.tsx
index e29169d419..f42a827936 100644
--- a/plugins/linear-genome-view/src/LinearGenomeView/components/RefNameAutocomplete/AutocompleteTextField.tsx
+++ b/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
diff --git a/plugins/linear-genome-view/src/LinearGenomeView/components/SearchResultsTable.tsx b/plugins/linear-genome-view/src/LinearGenomeView/components/SearchResultsTable.tsx
index 9b5fe78ba7..906ba1ad24 100644
--- a/plugins/linear-genome-view/src/LinearGenomeView/components/SearchResultsTable.tsx
+++ b/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 (
diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/components/util.ts b/plugins/spreadsheet-view/src/SpreadsheetView/components/util.ts
index 87a73ef9e1..6eefb3508a 100644
--- a/plugins/spreadsheet-view/src/SpreadsheetView/components/util.ts
+++ b/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
diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/BedpeImport.ts b/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/BedpeImport.ts
index 3977d98ab0..9ac70d39dd 100644
--- a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/BedpeImport.ts
+++ b/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)
diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/components/BreakendMultiLevelOptionDialog.tsx b/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/components/BreakendMultiLevelOptionDialog.tsx
new file mode 100644
index 0000000000..f2aedc807b
--- /dev/null
+++ b/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'
diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/components/BreakendSingleLevelOptionDialog.tsx b/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/components/BreakendSingleLevelOptionDialog.tsx
new file mode 100644
index 0000000000..e7bdfdc631
--- /dev/null
+++ b/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'
diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/components/FeatureMenu.tsx b/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/components/FeatureMenu.tsx
index bfe8cb9f9e..8c13e8e415 100644
--- a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/components/FeatureMenu.tsx
+++ b/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/components/FeatureMenu.tsx
@@ -1,5 +1,5 @@
-import React from 'react'
-import { AbstractSessionModel, Feature, getEnv } from '@jbrowse/core/util'
+import React, { lazy } from 'react'
+import { AbstractSessionModel, Feature } from '@jbrowse/core/util'
 import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton'
 
 // icons
@@ -7,6 +7,15 @@ import ArrowDropDownIcon from '@mui/icons-material/ArrowDropDown'
 
 // locals
 import { locationLinkClick } from '../../components/util'
+import { getEnv } from 'mobx-state-tree'
+
+// lazies
+const BreakendMultiLevelOptionDialog = lazy(
+  () => import('./BreakendMultiLevelOptionDialog'),
+)
+const BreakendSingleLevelOptionDialog = lazy(
+  () => import('./BreakendSingleLevelOptionDialog'),
+)
 
 export default function FeatureMenu({
   assemblyName,
@@ -48,41 +57,35 @@ export default function FeatureMenu({
         {
           label: 'Open in single-level split view',
           onClick: async () => {
-            try {
-              const { pluginManager } = getEnv(session)
-              const viewType = pluginManager.getViewType('BreakpointSplitView')!
-              const snap =
-                // @ts-expect-error
-                await viewType.singleLevelSnapshotFromBreakendFeature({
-                  feature: row.feature,
-                  session,
-                  assemblyName,
-                })
-              console.log({ snap })
-              session.addView('BreakpointSplitView', snap)
-            } catch (e) {
-              console.error(e)
-              session.notifyError(`${e}`, e)
-            }
+            const { pluginManager } = getEnv(session)
+            const viewType = pluginManager.getViewType('BreakpointSplitView')!
+            session.queueDialog(handleClose => [
+              BreakendSingleLevelOptionDialog,
+              {
+                handleClose,
+                session,
+                feature: row.feature,
+                viewType,
+                assemblyName,
+              },
+            ])
           },
         },
         {
           label: 'Open in multi-level split view',
           onClick: async () => {
-            try {
-              const { pluginManager } = getEnv(session)
-              const viewType = pluginManager.getViewType('BreakpointSplitView')!
-              // @ts-expect-error
-              const snap = await viewType.snapshotFromBreakendFeature({
-                feature: row.feature,
+            const { pluginManager } = getEnv(session)
+            const viewType = pluginManager.getViewType('BreakpointSplitView')!
+            session.queueDialog(handleClose => [
+              BreakendMultiLevelOptionDialog,
+              {
+                handleClose,
                 session,
+                feature: row.feature,
+                viewType,
                 assemblyName,
-              })
-              session.addView('BreakpointSplitView', snap)
-            } catch (e) {
-              console.error(e)
-              session.notifyError(`${e}`, e)
-            }
+              },
+            ])
           },
         },
       ]}
diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/components/LocString.tsx b/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/components/LocString.tsx
index e9a7fe3a37..93d4f9808f 100644
--- a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/components/LocString.tsx
+++ b/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/components/LocString.tsx
@@ -1,6 +1,6 @@
 import React from 'react'
 import { Link } from '@mui/material'
-import { AbstractSessionModel, getSession } from '@jbrowse/core/util'
+import { AbstractSessionModel } from '@jbrowse/core/util'
 
 // locals
 import { locationLinkClick } from '../../components/util'
diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/models/ImportWizard.ts b/plugins/spreadsheet-view/src/SpreadsheetView/models/ImportWizard.ts
index a2ef5f40ed..8db5ce6f55 100644
--- a/plugins/spreadsheet-view/src/SpreadsheetView/models/ImportWizard.ts
+++ b/plugins/spreadsheet-view/src/SpreadsheetView/models/ImportWizard.ts
@@ -156,7 +156,7 @@ function stateModelFactory() {
               }
               const buffer = await f.readFile()
               const buf2 = self.requiresUnzip ? await unzip(buffer) : buffer
-              const spreadsheet = await typeParser(buf2)
+              const spreadsheet = typeParser(buf2)
               getParent<any>(self).displaySpreadsheet(
                 spreadsheet,
                 self.selectedAssemblyName,
diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/models/SpreadsheetView.ts b/plugins/spreadsheet-view/src/SpreadsheetView/models/SpreadsheetView.ts
index 8564a8ea34..bf47e00060 100644
--- a/plugins/spreadsheet-view/src/SpreadsheetView/models/SpreadsheetView.ts
+++ b/plugins/spreadsheet-view/src/SpreadsheetView/models/SpreadsheetView.ts
@@ -1,4 +1,4 @@
-import { types, getParent, Instance } from 'mobx-state-tree'
+import { types, Instance } from 'mobx-state-tree'
 import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes/models'
 import { getSession } from '@jbrowse/core/util'
 
diff --git a/plugins/sv-inspector/src/SvInspectorView/models/SvInspectorView.ts b/plugins/sv-inspector/src/SvInspectorView/models/SvInspectorView.ts
index f6b259d88c..eace9b4bf5 100644
--- a/plugins/sv-inspector/src/SvInspectorView/models/SvInspectorView.ts
+++ b/plugins/sv-inspector/src/SvInspectorView/models/SvInspectorView.ts
@@ -1,25 +1,17 @@
 import clone from 'clone'
-import { autorun } from 'mobx'
-import { types, getParent, addDisposer, Instance } from 'mobx-state-tree'
+import { autorun, trace } from 'mobx'
+import { types, addDisposer, Instance } from 'mobx-state-tree'
 
 import PluginManager from '@jbrowse/core/PluginManager'
-import { getSession, notEmpty, Region } from '@jbrowse/core/util'
+import { getSession, notEmpty } from '@jbrowse/core/util'
 import { ElementId } from '@jbrowse/core/util/types/mst'
 import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes/models'
 import { SpreadsheetViewStateModel } from '@jbrowse/plugin-spreadsheet-view'
 import { CircularViewStateModel } from '@jbrowse/plugin-circular-view'
 
 // icons
-// import OpenInNewIcon from '@mui/icons-material/OpenInNew'
 import FolderOpenIcon from '@mui/icons-material/FolderOpen'
 
-// locals
-// import {
-//   canOpenBreakpointSplitViewFromTableRow,
-//   openBreakpointSplitViewFromTableRow,
-//   getFeatureForRow,
-// } from './breakpointSplitViewFromTableRow'
-
 /**
  * #stateModel SvInspectorView
  * #category view
@@ -139,10 +131,12 @@ function SvInspectorViewF(pluginManager: PluginManager) {
        * #getter
        */
       get featuresAdapterConfigSnapshot() {
-        return {
-          type: 'FromConfigAdapter',
-          features: this.features?.map(f => f.toJSON()) || [],
-        }
+        return this.features
+          ? {
+              type: 'FromConfigAdapter',
+              features: this.features.map(f => f.toJSON()) || [],
+            }
+          : undefined
       },
       /**
        * #getter
@@ -176,24 +170,26 @@ function SvInspectorViewF(pluginManager: PluginManager) {
        * #getter
        */
       get featuresCircularTrackConfiguration() {
-        return {
-          type: 'VariantTrack',
-          trackId: `sv-inspector-variant-track-${self.id}`,
-          name: 'features from tabular data',
-          adapter: this.featuresAdapterConfigSnapshot,
-          assemblyNames: [this.assemblyName],
-          displays: [
-            {
-              type: 'ChordVariantDisplay',
-              displayId: `sv-inspector-variant-track-chord-display-${self.id}`,
-              onChordClick:
-                'jexl:defaultOnChordClick(feature, track, pluginManager)',
-              renderer: {
-                type: 'StructuralVariantChordRenderer',
-              },
-            },
-          ],
-        }
+        return this.featuresAdapterConfigSnapshot
+          ? {
+              type: 'VariantTrack',
+              trackId: `sv-inspector-variant-track-${self.id}`,
+              name: 'features from tabular data',
+              adapter: this.featuresAdapterConfigSnapshot,
+              assemblyNames: [this.assemblyName],
+              displays: [
+                {
+                  type: 'ChordVariantDisplay',
+                  displayId: `sv-inspector-variant-track-chord-display-${self.id}`,
+                  onChordClick:
+                    'jexl:defaultOnChordClick(feature, track, pluginManager)',
+                  renderer: {
+                    type: 'StructuralVariantChordRenderer',
+                  },
+                },
+              ],
+            }
+          : undefined
       },
     }))
     .actions(self => ({
@@ -279,23 +275,20 @@ function SvInspectorViewF(pluginManager: PluginManager) {
               assembly,
             } = self
             try {
-              const { tracks } = circularView
               if (circularView.volatileWidth === undefined) {
                 return
               }
               if (assembly?.regions && featureRefSet) {
                 if (onlyDisplayRelevantRegionsInCircularView) {
-                  if (tracks.length === 1) {
-                    circularView.setDisplayedRegions(
-                      clone(
-                        assembly.regions.filter(r =>
-                          featureRefSet.has(r.refName),
-                        ),
+                  circularView.setDisplayedRegions(
+                    clone(
+                      assembly.regions.filter(r =>
+                        featureRefSet.has(r.refName),
                       ),
-                    )
-                  }
+                    ),
+                  )
                 } else {
-                  circularView.setDisplayedRegions(assembly?.regions)
+                  circularView.setDisplayedRegions(assembly.regions)
                 }
               }
             } catch (e) {
@@ -308,14 +301,10 @@ function SvInspectorViewF(pluginManager: PluginManager) {
         addDisposer(
           self,
           autorun(() => {
-            const { assemblyName, featuresCircularTrackConfiguration } = self
+            const { featuresCircularTrackConfiguration } = self
             const { circularView } = self
-            // hide any visible tracks
-            circularView.tracks.forEach(t =>
-              circularView.hideTrack(t.configuration.trackId),
-            )
-            // put our track in as the only track
-            if (assemblyName) {
+            if (featuresCircularTrackConfiguration) {
+              circularView.clearTracks()
               circularView.addTrackConf(featuresCircularTrackConfiguration)
             }
           }),
diff --git a/plugins/variants/src/VariantFeatureWidget/LaunchBreakendPanel.tsx b/plugins/variants/src/VariantFeatureWidget/LaunchBreakendPanel.tsx
index 26c0c8da1c..ee6776a4ef 100644
--- a/plugins/variants/src/VariantFeatureWidget/LaunchBreakendPanel.tsx
+++ b/plugins/variants/src/VariantFeatureWidget/LaunchBreakendPanel.tsx
@@ -51,7 +51,7 @@ function LocStringList({
                   }
                 } catch (e) {
                   console.error(e)
-                  session.notify(`${e}`)
+                  session.notifyError(`${e}`, e)
                 }
               }}
             >
@@ -92,7 +92,7 @@ function LaunchBreakpointSplitViewPanel({
                   BreakendMultiLevelOptionDialog,
                   {
                     handleClose,
-                    model,
+                    session,
                     feature: simpleFeature,
                     // @ts-expect-error
                     viewType,
@@ -112,7 +112,7 @@ function LaunchBreakpointSplitViewPanel({
                   BreakendSingleLevelOptionDialog,
                   {
                     handleClose,
-                    model,
+                    session,
                     feature: simpleFeature,
                     // @ts-expect-error
                     viewType,
diff --git a/products/jbrowse-aws-lambda-functions/saved-sessions/jbrowse_analytics.js b/products/jbrowse-aws-lambda-functions/saved-sessions/jbrowse_analytics.js
index 257bee76bf..5f7f50a856 100644
--- a/products/jbrowse-aws-lambda-functions/saved-sessions/jbrowse_analytics.js
+++ b/products/jbrowse-aws-lambda-functions/saved-sessions/jbrowse_analytics.js
@@ -15,7 +15,7 @@ function recordStats(event, context, done) {
   stats.referer = headers.Referer || headers.referer || null
   stats.acceptLanguage = headers['Accept-Language'] || null
   stats.acceptCharset = headers['Accept-Charset'] || null
-  // eslint-disable-next-line @typescript-eslint/no-deprecated
+   
   stats.host = stats.referer ? url_parser.parse(stats.referer).host : null
   if (stats.host?.startsWith('www.')) {
     stats.host = stats.host.slice(4)
diff --git a/products/jbrowse-desktop/src/indexJobsModel.ts b/products/jbrowse-desktop/src/indexJobsModel.ts
index 02196dd7a5..b672632a58 100644
--- a/products/jbrowse-desktop/src/indexJobsModel.ts
+++ b/products/jbrowse-desktop/src/indexJobsModel.ts
@@ -317,19 +317,10 @@ export default function jobsModelFactory(_pluginManager: PluginManager) {
           if (isAbortException(e)) {
             self.session?.notify('Cancelled job', 'info')
           } else {
-            self.session?.notify(
-              `An error occurred while indexing: ${e}`,
-              'error',
-              {
-                name: 'Retry',
-                onClick: () => {
-                  this.queueJob(entry)
-                },
-              },
-            )
+            self.session?.notifyError(`${e}`, e)
           }
-          // remove job from queue but since it was not successful
-          // do not add to finished list
+          // remove job from queue but since it was not successful do not add
+          // to finished list
           this.dequeueJob()
         }
         // clear
diff --git a/products/jbrowse-web/src/SessionLoader.ts b/products/jbrowse-web/src/SessionLoader.ts
index c53b8568a6..023c86169d 100644
--- a/products/jbrowse-web/src/SessionLoader.ts
+++ b/products/jbrowse-web/src/SessionLoader.ts
@@ -446,7 +446,7 @@ export function loadSessionSpec(
       )
     } catch (e) {
       console.error(e)
-      rootModel.session?.notify(`${e}`)
+      rootModel.session?.notifyError(`${e}`, e)
     }
   }
 }
diff --git a/products/jbrowse-web/src/components/JBrowse.tsx b/products/jbrowse-web/src/components/JBrowse.tsx
index c92b744130..586f653f25 100644
--- a/products/jbrowse-web/src/components/JBrowse.tsx
+++ b/products/jbrowse-web/src/components/JBrowse.tsx
@@ -54,7 +54,8 @@ const JBrowse = observer(function ({
           throw new Error(`HTTP ${response.status} (${message})`)
         }
       } catch (e) {
-        session?.notify(`Admin server error: ${e}`)
+        console.error(e)
+        session?.notifyError(`Admin server error: ${e}`, e)
       }
     })
   }, [jbrowse, session, adminKey, adminServer, configPath])
diff --git a/products/jbrowse-web/src/tests/SVInspector.test.tsx b/products/jbrowse-web/src/tests/SVInspector.test.tsx
index 0ef50befd8..4e426bc1d5 100644
--- a/products/jbrowse-web/src/tests/SVInspector.test.tsx
+++ b/products/jbrowse-web/src/tests/SVInspector.test.tsx
@@ -14,7 +14,6 @@ test(
   'opens a vcf.gz file in the sv inspector view',
   () =>
     mockConsoleWarn(async () => {
-      const consoleMock = jest.spyOn(console, 'warn').mockImplementation()
       const { session, findByTestId, getByTestId, findByText } =
         await createView()
 
@@ -36,8 +35,6 @@ test(
       // confirm breakpoint split view opened
       expect(session.views.length).toBe(3)
       expect(session.views[2]!.displayName).toBe('bnd_A split detail')
-
-      consoleMock.mockRestore()
     }),
   60000,
 )