Revert "Misc"

This reverts commit c4e16eb.

packages/core/pluggableElementTypes/renderers/BoxRendererType.ts

@@ -189,16 +189,16 @@ export default class BoxRendererType extends FeatureRendererType {
       args,
     ) as ResultsSerialized
 
-    return {
-      ...serialized,
-      layout: results.layout.serializeRegion(
-        this.getExpandedRegion(args.regions[0]!, args),
-      ),
-      maxHeightReached: serialized.layout.maxHeightReached,
-      features: serialized.features.filter(
-        f => !!serialized.layout.rectangles[f.uniqueId],
-      ),
-    }
+    const region = args.regions[0]!
+    serialized.layout = results.layout.serializeRegion(
+      this.getExpandedRegion(region, args),
+    )
+    serialized.features = serialized.features.filter(f => {
+      return Boolean(serialized.layout.rectangles[f.uniqueId])
+    })
+
+    serialized.maxHeightReached = serialized.layout.maxHeightReached
+    return serialized
   }
 
   /**

packages/core/pluggableElementTypes/renderers/ServerSideRendererType.tsx

@@ -87,26 +87,34 @@ export default class ServerSideRenderer extends RendererType {
    * @param results - the results of the render
    * @param args - the arguments passed to render
    */
-  deserializeResultsInClient(res: ResultsSerialized, args: RenderArgs) {
-    // if we are rendering svg, we skip hydration and check if rendere support
-    // SVG (e.g. this.supportsSVG) and then return just the HTML if so
-    return args.exportSVG
-      ? {
-          ...res,
-          html: this.supportsSVG
-            ? res.html
-            : '<text y="12" fill="black">SVG export not supported for this track</text>',
-        }
-      : {
-          ...res,
-          reactElement: (
-            <ServerSideRenderedContent
-              {...args}
-              {...res}
-              RenderingComponent={this.ReactComponent}
-            />
-          ),
-        }
+  deserializeResultsInClient(
+    res: ResultsSerialized,
+    args: RenderArgs,
+  ): ResultsDeserialized {
+    // if we are rendering svg, we skip hydration
+    if (args.exportSVG) {
+      // only return the res if the renderer explicitly has
+      // this.supportsSVG support to avoid garbage being rendered in SVG
+      // document
+      return {
+        ...res,
+        html: this.supportsSVG
+          ? res.html
+          : '<text y="12" fill="black">SVG export not supported for this track</text>',
+      }
+    }
+
+    // get res using ServerSideRenderedContent
+    return {
+      ...res,
+      reactElement: (
+        <ServerSideRenderedContent
+          {...args}
+          {...res}
+          RenderingComponent={this.ReactComponent}
+        />
+      ),
+    }
   }
 
   /**
@@ -115,17 +123,18 @@ export default class ServerSideRenderer extends RendererType {
    *
    * @param args - the converted arguments to modify
    */
-  deserializeArgsInWorker(args: RenderArgsSerialized) {
-    console.log('deserializeArgsInWorker', { args })
-    return {
-      ...args,
-      config: this.configSchema.create(args.config || {}, {
-        pluginManager: this.pluginManager,
-      }),
-      filters: args.filters
-        ? new SerializableFilterChain({ filters: args.filters })
-        : undefined,
-    }
+  deserializeArgsInWorker(args: RenderArgsSerialized): RenderArgsDeserialized {
+    const deserialized = { ...args } as unknown as RenderArgsDeserialized
+    deserialized.config = this.configSchema.create(args.config || {}, {
+      pluginManager: this.pluginManager,
+    })
+    deserialized.filters = args.filters
+      ? new SerializableFilterChain({
+          filters: args.filters,
+        })
+      : undefined
+
+    return deserialized
   }
 
   /**
@@ -206,4 +215,4 @@ export default class ServerSideRenderer extends RendererType {
   }
 }
 
-export type { RenderResults } from './RendererType'
+export { type RenderResults } from './RendererType'

plugins/breakpoint-split-view/src/BreakpointAlignmentsFeatureDetail/BreakpointAlignmentsFeatureDetail.tsx

@@ -6,15 +6,22 @@ import {
 } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail'
 import { Paper } from '@mui/material'
 import { observer } from 'mobx-react'
+import { SimpleFeatureSerialized } from '@jbrowse/core/util'
 
 const BreakpointAlignmentsFeatureDetail = observer(function ({
   model,
 }: {
-  model: { featureData: Record<string, unknown> }
+  model: {
+    featureData: {
+      feature1: SimpleFeatureSerialized
+      feature2: SimpleFeatureSerialized
+    }
+  }
 }) {
-  const { feature1, feature2 } = JSON.parse(JSON.stringify(model.featureData))
+  const { featureData } = model
+  const { feature1, feature2 } = structuredClone(featureData)
   return (
-    <Paper data-testid="alignment-side-drawer">
+    <Paper>
       <BaseCoreDetails title="Feature 1" feature={feature1} />
       <BaseCoreDetails title="Feature 2" feature={feature2} />
       <BaseAttributes title="Feature 1 attributes" feature={feature1} />

plugins/linear-comparative-view/src/SyntenyFeatureDetail/SyntenyFeatureDetail.tsx

@@ -114,7 +114,7 @@ const SyntenyFeatureDetail = observer(function ({
   model: SyntenyFeatureDetailModel
 }) {
   return (
-    <Paper data-testid="alignment-side-drawer">
+    <Paper>
       <BaseFeatureDetail title="Feature" model={model} />
       <BaseCard title="Link to view">
         <CustomLinker model={model} />

plugins/variants/src/MultiLinearVariantDisplay/model.ts

@@ -22,9 +22,7 @@ import type { Instance } from 'mobx-state-tree'
 // lazies
 const Tooltip = lazy(() => import('../shared/Tooltip'))
 const SetColorDialog = lazy(() => import('../shared/SetColorDialog'))
-const HierarchicalClusterDialog = lazy(
-  () => import('../shared/HierarchicalClusterDialog'),
-)
+const ClusterDialog = lazy(() => import('../shared/ClusterDialog'))
 
 // using a map because it preserves order
 const rendererTypes = new Map([['multivariant', 'MultiVariantRenderer']])
@@ -263,7 +261,7 @@ export function stateModelFactory(
               label: 'Cluster by genotype',
               onClick: () => {
                 getSession(self).queueDialog(handleClose => [
-                  HierarchicalClusterDialog,
+                  ClusterDialog,
                   {
                     model: self,
                     handleClose,

plugins/variants/src/MultiLinearVariantMatrixDisplay/components/VariantDisplayComponent.tsx

@@ -15,6 +15,7 @@ import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 const useStyles = makeStyles()({
   cursor: {
     pointerEvents: 'none',
+    zIndex: 1000,
   },
 })
 

plugins/variants/src/MultiLinearVariantMatrixDisplay/model.ts

@@ -19,9 +19,7 @@ import type { Instance } from 'mobx-state-tree'
 // lazies
 const SetColorDialog = lazy(() => import('../shared/SetColorDialog'))
 const MAFFilterDialog = lazy(() => import('../shared/MAFFilterDialog'))
-const HierarchicalClusterDialog = lazy(
-  () => import('../shared/HierarchicalClusterDialog'),
-)
+const ClusterDialog = lazy(() => import('../shared/ClusterDialog'))
 
 /**
  * #stateModel LinearVariantMatrixDisplay
@@ -176,7 +174,7 @@ export default function stateModelFactory(
               label: 'Cluster by genotype',
               onClick: () => {
                 getSession(self).queueDialog(handleClose => [
-                  HierarchicalClusterDialog,
+                  ClusterDialog,
                   {
                     model: self,
                     handleClose,
@@ -252,6 +250,21 @@ export default function stateModelFactory(
               }
             }
           })()
+
+          // eslint-disable-next-line @typescript-eslint/no-floating-promises
+          ;(async () => {
+            try {
+              const { getMultiVariantSourcesAutorun } = await import(
+                '../getMultiVariantSourcesAutorun'
+              )
+              getMultiVariantSourcesAutorun(self)
+            } catch (e) {
+              if (isAlive(self)) {
+                console.error(e)
+                getSession(self).notifyError(`${e}`, e)
+              }
+            }
+          })()
         },
 
         /**

plugins/variants/src/MultiLinearVariantMatrixRenderer/components/LinearVariantMatrixRendering.tsx

@@ -17,11 +17,11 @@ const LinearVariantMatrixRendering = observer(function (props: {
   regions: Region[]
   bpPerPx: number
   simplifiedFeatures: Feature[]
-  exportSVG: boolean
   onMouseMove?: (event: React.MouseEvent, featureId?: string) => void
 }) {
-  const { exportSVG, simplifiedFeatures, displayModel, width, height } = props
-  const [renderLines, setRenderLines] = useState(exportSVG)
+  const { simplifiedFeatures, displayModel, width, height } = props
+  console.log('Rendering', props.regions)
+  const [renderLines, setRenderLines] = useState(false)
   useEffect(() => {
     setRenderLines(true)
   }, [])

plugins/variants/src/VariantRPC/MultiVariantGetHierarchicalMatrix.ts → plugins/variants/src/VariantRPC/MultiVariantGetGenotypeMatrix.ts

@@ -9,8 +9,8 @@ import type { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAda
 import type { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods'
 import type { Feature, Region } from '@jbrowse/core/util'
 
-export class MultiVariantGetHierarchicalMatrix extends RpcMethodType {
-  name = 'MultiVariantGetHierarchicalMatrix'
+export class MultiVariantGetGenotypeMatrix extends RpcMethodType {
+  name = 'MultiVariantGetGenotypeMatrix'
 
   async deserializeArguments(args: any, rpcDriverClassName: string) {
     const l = await super.deserializeArguments(args, rpcDriverClassName)

plugins/variants/src/VariantRPC/MultiVariantGetSimplifiedFeatures.ts

@@ -0,0 +1,76 @@
+import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache'
+import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType'
+import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain'
+import { renameRegionsIfNeeded } from '@jbrowse/core/util'
+
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration'
+import type { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods'
+import type { Region } from '@jbrowse/core/util'
+import { toArray } from 'rxjs'
+
+export class MultiVariantGetSimplifiedFeatures extends RpcMethodType {
+  name = 'MultiVariantGetSimplifiedFeatures'
+
+  async deserializeArguments(args: any, rpcDriverClassName: string) {
+    const l = await super.deserializeArguments(args, rpcDriverClassName)
+    return {
+      ...l,
+      filters: args.filters
+        ? new SerializableFilterChain({
+            filters: args.filters,
+          })
+        : undefined,
+    }
+  }
+
+  async serializeArguments(
+    args: RenderArgs & {
+      stopToken?: string
+      statusCallback?: (arg: string) => void
+    },
+    rpcDriverClassName: string,
+  ) {
+    const pm = this.pluginManager
+    const assemblyManager = pm.rootModel?.session?.assemblyManager
+    if (!assemblyManager) {
+      return args
+    }
+
+    const renamedArgs = await renameRegionsIfNeeded(assemblyManager, {
+      ...args,
+      filters: args.filters?.toJSON().filters,
+    })
+
+    return super.serializeArguments(renamedArgs, rpcDriverClassName)
+  }
+
+  async execute(
+    args: {
+      adapterConfig: AnyConfigurationModel
+      stopToken?: string
+      sessionId: string
+      headers?: Record<string, string>
+      regions: Region[]
+      bpPerPx: number
+    },
+    rpcDriverClassName: string,
+  ) {
+    const pm = this.pluginManager
+    const deserializedArgs = await this.deserializeArguments(
+      args,
+      rpcDriverClassName,
+    )
+    const { regions, adapterConfig, sessionId } = deserializedArgs
+    const { dataAdapter } = await getAdapter(pm, sessionId, adapterConfig)
+
+    // @ts-expect-error
+    const feats = await firstValuFrom(
+      dataAdapter.getFeatures(regions, deserializedArgs).pipe(toArray()),
+    )
+    return feats.map(f => ({
+      start: f.get('start'),
+      end: f.get('end'),
+      refName: f.get('refName'),
+    }))
+  }
+}

plugins/variants/src/getMultiVariantSourcesAutorun.ts

@@ -42,7 +42,41 @@ export function getMultiVariantSourcesAutorun(self: {
           sessionId,
           'MultiVariantGetSources',
           {
-            regions: view.staticBlocks.contentBlocks,
+            regions: view.dynamicBlocks.contentBlocks,
+            sessionId,
+            adapterConfig,
+          },
+        )) as Source[]
+        if (isAlive(self)) {
+          self.setSources(sources)
+        }
+      } catch (e) {
+        if (!isAbortException(e) && isAlive(self)) {
+          console.error(e)
+          getSession(self).notifyError(`${e}`, e)
+        }
+      }
+    }),
+  )
+
+  addDisposer(
+    self,
+    autorun(async () => {
+      try {
+        const view = getContainingView(self) as LinearGenomeViewModel
+        if (!view.initialized) {
+          return
+        }
+        const { rpcManager } = getSession(self)
+        const { adapterConfig } = self
+        const token = createStopToken()
+        self.setSourcesLoading(token)
+        const sessionId = getRpcSessionId(self)
+        const sources = (await rpcManager.call(
+          sessionId,
+          'MultiVariantGetSimplifiedFeatures',
+          {
+            regions: view.dynamicBlocks.contentBlocks,
             sessionId,
             adapterConfig,
           },

plugins/variants/src/index.ts

@@ -8,8 +8,9 @@ import LinearVariantMatrixRendererF from './MultiLinearVariantMatrixRenderer'
 import MultiVariantRendererF from './MultiLinearVariantRenderer'
 import StructuralVariantChordRendererF from './StructuralVariantChordRenderer'
 import VariantFeatureWidgetF from './VariantFeatureWidget'
-import { MultiVariantGetHierarchicalMatrix } from './VariantRPC/MultiVariantGetHierarchicalMatrix'
+import { MultiVariantGetGenotypeMatrix } from './VariantRPC/MultiVariantGetGenotypeMatrix'
 import { MultiVariantGetSources } from './VariantRPC/MultiVariantGetSources'
+import { MultiVariantGetSimplifiedFeatures } from './VariantRPC/MultiVariantGetSimplifiedFeatures'
 import VariantTrackF from './VariantTrack'
 import VcfAdapterF from './VcfAdapter'
 import VcfTabixAdapterF from './VcfTabixAdapter'
@@ -36,7 +37,10 @@ export default class VariantsPlugin extends Plugin {
 
     pluginManager.addRpcMethod(() => new MultiVariantGetSources(pluginManager))
     pluginManager.addRpcMethod(
-      () => new MultiVariantGetHierarchicalMatrix(pluginManager),
+      () => new MultiVariantGetGenotypeMatrix(pluginManager),
+    )
+    pluginManager.addRpcMethod(
+      () => new MultiVariantGetSimplifiedFeatures(pluginManager),
     )
   }
 }