Fix retrieval of VCF metadata for tooltips in VCF feature details (#4845

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GMOD · Feb 15, 2025 · f03393a · f03393a
1 parent be4e0a1
commit f03393a
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Showing 10 changed files with 13 additions and 4 deletions.
diff --git a/...Widget/BreakendMultiLevelOptionDialog.tsx → ...dPanel/BreakendMultiLevelOptionDialog.tsx b/...Widget/BreakendMultiLevelOptionDialog.tsx → ...dPanel/BreakendMultiLevelOptionDialog.tsx
diff --git a/...idget/BreakendSingleLevelOptionDialog.tsx → ...Panel/BreakendSingleLevelOptionDialog.tsx b/...idget/BreakendSingleLevelOptionDialog.tsx → ...Panel/BreakendSingleLevelOptionDialog.tsx
diff --git a/...iantFeatureWidget/LaunchBreakendPanel.tsx → ...unchBreakendPanel/LaunchBreakendPanel.tsx b/...iantFeatureWidget/LaunchBreakendPanel.tsx → ...unchBreakendPanel/LaunchBreakendPanel.tsx
@@ -4,7 +4,7 @@ import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard
 import { SimpleFeature, getEnv, getSession } from '@jbrowse/core/util'
 import { Link, Typography } from '@mui/material'
 
-import type { VariantFeatureWidgetModel } from './stateModelFactory'
+import type { VariantFeatureWidgetModel } from '../stateModelFactory'
 import type { SimpleFeatureSerialized } from '@jbrowse/core/util'
 
 // lazies

diff --git a/...eatureWidget/LaunchBreakendWidgetArea.tsx → ...reakendPanel/LaunchBreakendWidgetArea.tsx b/...eatureWidget/LaunchBreakendWidgetArea.tsx → ...reakendPanel/LaunchBreakendWidgetArea.tsx
@@ -2,7 +2,7 @@ import { Suspense, lazy } from 'react'
 
 import { parseBreakend } from '@gmod/vcf'
 
-import type { VariantFeatureWidgetModel } from './stateModelFactory'
+import type { VariantFeatureWidgetModel } from '../stateModelFactory'
 
 // lazies
 const LaunchBreakendPanel = lazy(() => import('./LaunchBreakendPanel'))

diff --git a/plugins/variants/src/VariantFeatureWidget/LaunchBreakendPanel/index.tsx b/plugins/variants/src/VariantFeatureWidget/LaunchBreakendPanel/index.tsx
@@ -0,0 +1 @@
+export { default } from './LaunchBreakendPanel'
diff --git a/plugins/variants/src/VariantFeatureWidget/VariantFeatureWidget.tsx b/plugins/variants/src/VariantFeatureWidget/VariantFeatureWidget.tsx
@@ -5,14 +5,16 @@ import FeatureDetails from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/Fe
 import { Paper } from '@mui/material'
 import { observer } from 'mobx-react'
 
-import VariantSampleGrid from './VariantSampleGrid'
+import VariantSampleGrid from './VariantSampleGrid/VariantSampleGrid'
 import { variantFieldDescriptions } from './variantFieldDescriptions'
 
 import type { VariantFeatureWidgetModel } from './stateModelFactory'
 import type { Descriptions, ReducedFeature } from './types'
 
 // lazies
-const LaunchBreakendPanel = lazy(() => import('./LaunchBreakendPanel'))
+const LaunchBreakendPanel = lazy(
+  () => import('./LaunchBreakendPanel/LaunchBreakendPanel'),
+)
 const VariantConsequenceDataGrid = lazy(
   () => import('./VariantConsequenceDataGrid'),
 )

diff --git a/...antFeatureWidget/VariantSampleFilters.tsx → ...ariantSampleGrid/VariantSampleFilters.tsx b/...antFeatureWidget/VariantSampleFilters.tsx → ...ariantSampleGrid/VariantSampleFilters.tsx
diff --git a/...ariantFeatureWidget/VariantSampleGrid.tsx → ...t/VariantSampleGrid/VariantSampleGrid.tsx b/...ariantFeatureWidget/VariantSampleGrid.tsx → ...t/VariantSampleGrid/VariantSampleGrid.tsx
diff --git a/plugins/variants/src/VariantFeatureWidget/VariantSampleGrid/index.tsx b/plugins/variants/src/VariantFeatureWidget/VariantSampleGrid/index.tsx
@@ -0,0 +1 @@
+export { default } from './VariantSampleGrid'
diff --git a/plugins/variants/src/VcfTabixAdapter/VcfTabixAdapter.ts b/plugins/variants/src/VcfTabixAdapter/VcfTabixAdapter.ts
@@ -69,6 +69,11 @@ export default class VcfTabixAdapter extends BaseFeatureDataAdapter {
     return vcf.getHeader()
   }
 
+  async getMetadata(opts?: BaseOptions) {
+    const { parser } = await this.configure(opts)
+    return parser.getMetadata()
+  }
+
   public getFeatures(query: NoAssemblyRegion, opts: BaseOptions = {}) {
     return ObservableCreate<Feature>(async observer => {
       const { refName, start, end } = query
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		export { default } from './LaunchBreakendPanel'