Misc

GMOD · Sep 24, 2024 · d551ec9 · d551ec9
1 parent 31c10b2
commit d551ec9
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Showing 7 changed files with 49 additions and 34 deletions.
diff --git a/plugins/breakpoint-split-view/src/BreakpointSplitView/BreakpointSplitView.ts b/plugins/breakpoint-split-view/src/BreakpointSplitView/BreakpointSplitView.ts
@@ -115,7 +115,7 @@ export default class BreakpointSplitViewType extends ViewType {
     const bpPerPx = 10
     const { assemblyManager } = session
     const assembly = await assemblyManager.waitForAssembly(assemblyName)
-    if (!assembly) {
+    if (!assembly?.regions) {
       throw new Error(`assembly ${assemblyName} not found`)
     }
 

diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/components/SpreadsheetView.tsx b/plugins/spreadsheet-view/src/SpreadsheetView/components/SpreadsheetView.tsx
@@ -32,7 +32,7 @@ const SpreadsheetView = observer(function ({
   const [initialHeight, setInitialHeight] = useState<number>(0)
   const { classes } = useStyles()
   const { spreadsheet, hideVerticalResizeHandle, height } = model
-  return (
+  return spreadsheet ? (
     <>
       <div style={{ height }} className={classes.contentArea}>
         <SpreadsheetDataGrid model={spreadsheet} />
@@ -47,6 +47,8 @@ const SpreadsheetView = observer(function ({
         />
       )}
     </>
+  ) : (
+    <div>Unknown</div>
   )
 })
 

diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/components/util.ts b/plugins/spreadsheet-view/src/SpreadsheetView/components/util.ts
@@ -1,19 +1,26 @@
-import { FileLocation, getSession } from '@jbrowse/core/util'
+import {
+  AbstractSessionModel,
+  FileLocation,
+  getSession,
+} from '@jbrowse/core/util'
 import { getParent } from 'mobx-state-tree'
 import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 
 type LGV = LinearGenomeViewModel
 type MaybeLGV = LinearGenomeViewModel | undefined
 
-export function locationLinkClick(
-  spreadsheet: { assemblyName?: string },
-  locString: string,
-) {
-  const session = getSession(spreadsheet)
-  const { assemblyName } = spreadsheet
-  const { id } = getParent<{ id: string }>(spreadsheet)
-
-  const newViewId = `${id}_${assemblyName}`
+export function locationLinkClick({
+  assemblyName,
+  session,
+  locString,
+  spreadsheetViewId,
+}: {
+  assemblyName: string
+  session: AbstractSessionModel
+  locString: string
+  spreadsheetViewId: string
+}) {
+  const newViewId = `${spreadsheetViewId}_${assemblyName}`
   let view = session.views.find(v => v.id === newViewId) as MaybeLGV
   if (!view) {
     view = session.addView('LinearGenomeView', { id: newViewId }) as LGV

diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/components/FeatureMenu.tsx b/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/components/FeatureMenu.tsx
@@ -11,17 +11,21 @@ import { locationLinkClick } from '../../components/util'
 export default function FeatureMenu({
   assemblyName,
   session,
-  row,
-  spreadsheetId,
+  arg,
+  spreadsheetViewId,
 }: {
-  spreadsheetId: string
+  spreadsheetViewId: string
   assemblyName: string
   session: AbstractSessionModel
-  row: {
-    feature: Feature
-    value: string
+  arg: {
+    value?: string
+    row: {
+      feature: Feature
+      loc: string
+    }
   }
 }) {
+  const { row } = arg
   return (
     <CascadingMenuButton
       menuItems={[
@@ -31,51 +35,53 @@ export default function FeatureMenu({
             try {
               await locationLinkClick({
                 spreadsheetViewId,
-                locString: row.value,
+                locString: row.loc,
                 assemblyName,
                 session,
               })
             } catch (e) {
               console.error(e)
-              session.notify(`${e}`, 'error')
+              session.notifyError(`${e}`, e)
             }
           },
         },
         {
-          label: 'Open in single level split view',
+          label: 'Open in single-level split view',
           onClick: async () => {
             try {
               const { pluginManager } = getEnv(session)
               const viewType = pluginManager.getViewType('BreakpointSplitView')!
-              // @ts-expect-error
-              const snap = viewType.singleLevelSnapshotFromBreakendFeature({
-                feature: row.feature,
-                session,
-                assemblyName,
-              })
+              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.notify(`${e}`, 'error')
+              session.notifyError(`${e}`, e)
             }
           },
         },
         {
-          label: 'Open in breakpoint split view',
+          label: 'Open in multi-level split view',
           onClick: async () => {
             try {
               const { pluginManager } = getEnv(session)
               const viewType = pluginManager.getViewType('BreakpointSplitView')!
               // @ts-expect-error
-              const snap = viewType.snapshotFromBreakendFeature({
+              const snap = await viewType.snapshotFromBreakendFeature({
                 feature: row.feature,
                 session,
                 assemblyName,
               })
               session.addView('BreakpointSplitView', snap)
             } catch (e) {
               console.error(e)
-              session.notify(`${e}`, 'error')
+              session.notifyError(`${e}`, e)
             }
           },
         },

diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/models/Spreadsheet.tsx b/plugins/spreadsheet-view/src/SpreadsheetView/models/Spreadsheet.tsx
@@ -111,8 +111,7 @@ function stateModelFactory() {
                 session={session}
                 spreadsheetViewId={getParent<{ id: string }>(self).id}
                 assemblyName={self.assemblyName}
-                // @ts-expect-error
-                row={row}
+                arg={row}
               />
             ),
           },

diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/models/SpreadsheetView.ts b/plugins/spreadsheet-view/src/SpreadsheetView/models/SpreadsheetView.ts
@@ -116,6 +116,7 @@ function stateModelFactory() {
        * load a new spreadsheet and set our mode to display it
        */
       displaySpreadsheet(spreadsheet: SpreadsheetData, assemblyName: string) {
+        // @ts-expect-error
         self.spreadsheet = { assemblyName }
         // @ts-expect-error
         self.spreadsheet.setData(spreadsheet)

diff --git a/plugins/sv-inspector/src/SvInspectorView/models/SvInspectorView.ts b/plugins/sv-inspector/src/SvInspectorView/models/SvInspectorView.ts
@@ -226,7 +226,7 @@ function SvInspectorViewF(pluginManager: PluginManager) {
           {
             label: 'Return to import form',
             onClick: () => {
-              self.spreadsheetView.spreadsheet.setData(undefined)
+              self.spreadsheetView.clearData()
             },
             icon: FolderOpenIcon,
           },