Volatile-ize spreadsheet view

Remove [skip ci] Volatile [skip ci] Parse out INFO field [skip ci] Misc Misc Restyling Refactoring More misc Misc Misc Misc Misc New Refname renaming fix for breakpoint split view Breakpoint split view Misc [skip ci] Refactors Use 7.0.0 Updates Misc Misc Misc SV inspector working Wow Misc More notifyError
GMOD · Nov 4, 2024 · 834ad10 · 834ad10
1 parent c5ba32e
commit 834ad10
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Showing 93 changed files with 1,428 additions and 29,414 deletions.
diff --git a/eslint.config.mjs b/eslint.config.mjs
@@ -141,6 +141,7 @@ 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/assemblyManager/assembly.ts b/packages/core/assemblyManager/assembly.ts
@@ -294,6 +294,12 @@ export default function assemblyFactory(
           self.refNameAliases[refName] || self.lowerCaseRefNameAliases[refName]
         )
       },
+      /**
+       * #method
+       */
+      getCanonicalRefNameOrDefault(refName: string) {
+        return this.getCanonicalRefName(refName) || refName
+      },
       /**
        * #method
        */

diff --git a/packages/core/assemblyManager/assemblyManager.ts b/packages/core/assemblyManager/assemblyManager.ts
@@ -153,9 +153,7 @@ function assemblyManagerFactory(conf: IAnyType, pm: PluginManager) {
         if (assembly) {
           return assembly.isValidRefName(refName)
         }
-        throw new Error(
-          `Failed to look up refName ${refName} on ${assemblyName} because assembly does not exist`,
-        )
+        throw new Error(`assembly "${assemblyName}" not found`)
       },
     }))
     .actions(self => ({

diff --git a/packages/core/configuration/util.ts b/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[],

diff --git a/packages/core/pluggableElementTypes/renderers/RpcRenderedSvgGroup.tsx b/packages/core/pluggableElementTypes/renderers/RpcRenderedSvgGroup.tsx
@@ -69,6 +69,7 @@ const OldHydrate = observer(function OldHydrate(props: Props) {
     function doHydrate() {
       if (domNode && html) {
         if (domNode.innerHTML) {
+
           unmountComponentAtNode(domNode)
         }
 
@@ -80,13 +81,15 @@ const OldHydrate = observer(function OldHydrate(props: Props) {
         // hydration for when we have some free time. helps keep the
         // framerate up.
         rIC(() => {
+
           hydrate(<RenderingComponent {...props} />, domNode)
         })
       }
     }
     doHydrate()
     return () => {
       if (domNode) {
+
         unmountComponentAtNode(domNode)
       }
     }

diff --git a/packages/core/pluggableElementTypes/renderers/ServerSideRenderedContent.tsx b/packages/core/pluggableElementTypes/renderers/ServerSideRenderedContent.tsx
@@ -82,10 +82,12 @@ const OldHydrate = observer(function ({
     const domNode = ref.current
     function doHydrate() {
       if (domNode) {
+
         unmountComponentAtNode(domNode)
         domNode.innerHTML = html
 
         rIC(() => {
+
           hydrate(
             <ThemeProvider theme={jbrowseTheme}>
               <RenderingComponent {...rest} />
@@ -100,6 +102,7 @@ const OldHydrate = observer(function ({
 
     return () => {
       if (domNode) {
+
         unmountComponentAtNode(domNode)
       }
     }

diff --git a/packages/core/ui/ResizeHandle.tsx b/packages/core/ui/ResizeHandle.tsx
@@ -12,11 +12,14 @@ const useStyles = makeStyles()({
   },
   flexbox_verticalHandle: {
     cursor: 'col-resize',
-    alignSelf: 'stretch', // the height: 100% is actually unable to function inside flexbox
+    alignSelf: 'stretch',
+    // uses alignSelf:stretch with flexbox as the height: 100% is actually
+    // unable to function inside flexbox
   },
   flexbox_horizontalHandle: {
     cursor: 'row-resize',
-    alignSelf: 'stretch', // similar to above
+    alignSelf: 'stretch',
+    // similar to above
   },
 })
 

diff --git a/packages/core/util/index.ts b/packages/core/util/index.ts
@@ -1458,6 +1458,7 @@ export function renderToStaticMarkup(
     if (createRootFn) {
       createRootFn(div).render(node)
     } else {
+
       render(node, div)
     }
   })

diff --git 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: {
@@ -63,45 +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()

diff --git 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
@@ -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
@@ -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)
               }
             },
           }