New files

packages/core/data_adapters/dataAdapterCache.ts

@@ -73,44 +73,39 @@ export async function getAdapter(
 }
 
 /**
- * this is a callback that is passed to adapters that
- * allows them to get any sub-adapters that they need
- * internally, staying with the same worker session ID
+ * this is a callback that is passed to adapters that allows them to get any
+ * sub-adapters that they need internally, staying with the same worker session
+ * ID
  */
 export type getSubAdapterType = (
   adapterConfigSnap: ConfigSnap,
 ) => ReturnType<typeof getAdapter>
 
-export function freeAdapterResources(specification: Record<string, any>) {
-  let deleteCount = 0
-  const specKeys = Object.keys(specification)
+export function freeAdapterResources(args: Record<string, any>) {
+  const specKeys = Object.keys(args)
 
+  // TODO: little hacky...should make it an explicit command but:
   // if we don't specify a range, delete any adapters that are only associated
   // with that session
   if (specKeys.length === 1 && specKeys[0] === 'sessionId') {
-    const { sessionId } = specification
+    const { sessionId } = args
     Object.entries(adapterCache).forEach(([cacheKey, cacheEntry]) => {
       cacheEntry.sessionIds.delete(sessionId)
       if (cacheEntry.sessionIds.size === 0) {
-        deleteCount += 1
         delete adapterCache[cacheKey]
       }
     })
   } else {
     // otherwise call freeResources on all the cached data adapters
     Object.values(adapterCache).forEach(cacheEntry => {
-      const regions =
-        specification.regions ||
-        (specification.region ? [specification.region] : [])
+      const regions = args.regions || (args.region ? [args.region] : [])
       for (const region of regions) {
         if (region.refName !== undefined) {
           cacheEntry.dataAdapter.freeResources(region)
         }
       }
     })
   }
-
-  return deleteCount
 }
 
 export function clearAdapterCache() {

packages/core/pluggableElementTypes/renderers/BoxRendererType.ts

@@ -1,11 +1,8 @@
-import deepEqual from 'fast-deep-equal'
-
 // layouts
 import FeatureRendererType from './FeatureRendererType'
+import { LayoutSession } from './LayoutSession'
 import { readConfObject } from '../../configuration'
 import { getLayoutId } from '../../util'
-import GranularRectLayout from '../../util/layouts/GranularRectLayout'
-import MultiLayout from '../../util/layouts/MultiLayout'
 import PrecomputedLayout from '../../util/layouts/PrecomputedLayout'
 
 // other
@@ -17,81 +14,18 @@ import type {
   ResultsDeserialized as FeatureResultsDeserialized,
   ResultsSerialized as FeatureResultsSerialized,
 } from './FeatureRendererType'
-import type { AnyConfigurationModel } from '../../configuration'
-import type { Feature, Region } from '../../util'
-import type SerializableFilterChain from './util/serializableFilterChain'
+import type { LayoutSessionProps } from './LayoutSession'
 import type RpcManager from '../../rpc/RpcManager'
+import type { Feature, Region } from '../../util'
 import type {
   BaseLayout,
   SerializedLayout,
 } from '../../util/layouts/BaseLayout'
-
-export interface LayoutSessionProps {
-  config: AnyConfigurationModel
-  bpPerPx: number
-  filters?: SerializableFilterChain
-}
+import type GranularRectLayout from '../../util/layouts/GranularRectLayout'
+import type MultiLayout from '../../util/layouts/MultiLayout'
 
 export type MyMultiLayout = MultiLayout<GranularRectLayout<unknown>, unknown>
 
-export interface CachedLayout {
-  layout: MyMultiLayout
-  config: AnyConfigurationModel
-  filters?: SerializableFilterChain
-}
-
-export class LayoutSession implements LayoutSessionProps {
-  config: AnyConfigurationModel
-
-  bpPerPx: number
-
-  filters?: SerializableFilterChain
-
-  constructor(args: LayoutSessionProps) {
-    this.config = args.config
-    this.bpPerPx = args.bpPerPx
-    this.filters = args.filters
-    this.update(args)
-  }
-
-  update(props: LayoutSessionProps) {
-    Object.assign(this, props)
-  }
-
-  makeLayout() {
-    return new MultiLayout(GranularRectLayout, {
-      maxHeight: readConfObject(this.config, 'maxHeight'),
-      displayMode: readConfObject(this.config, 'displayMode'),
-      pitchX: this.bpPerPx,
-      pitchY: readConfObject(this.config, 'noSpacing') ? 1 : 3,
-    })
-  }
-
-  /**
-   * @param layout -
-   * @returns true if the given layout is a valid one to use for this session
-   */
-  cachedLayoutIsValid(cachedLayout: CachedLayout) {
-    return (
-      cachedLayout.layout.subLayoutConstructorArgs.pitchX === this.bpPerPx &&
-      deepEqual(readConfObject(this.config), cachedLayout.config) &&
-      deepEqual(this.filters, cachedLayout.filters)
-    )
-  }
-
-  cachedLayout: CachedLayout | undefined
-
-  get layout(): MyMultiLayout {
-    if (!this.cachedLayout || !this.cachedLayoutIsValid(this.cachedLayout)) {
-      this.cachedLayout = {
-        layout: this.makeLayout(),
-        config: readConfObject(this.config),
-        filters: this.filters,
-      }
-    }
-    return this.cachedLayout.layout
-  }
-}
 export interface RenderArgs extends FeatureRenderArgs {
   bpPerPx: number
   layoutId: string
@@ -128,11 +62,9 @@ export default class BoxRendererType extends FeatureRendererType {
   ) {
     const key = getLayoutId(props)
     if (!this.sessions[key]) {
-      this.sessions[key] = this.createSession(props)
+      this.sessions[key] = new LayoutSession(props)
     }
-    const session = this.sessions[key]
-    session.update(props)
-    return session
+    return this.sessions[key].update(props)
   }
 
   getExpandedRegion(region: Region, renderArgs: RenderArgsDeserialized) {
@@ -147,19 +79,34 @@ export default class BoxRendererType extends FeatureRendererType {
     }
   }
 
-  createSession(props: LayoutSessionProps) {
-    return new LayoutSession(props)
+  freeResources(args: Record<string, any>) {
+    // renaming function to make clear it runs in worker
+    this.freeResourcesInWorker(args)
+  }
+
+  freeResourcesInWorker(args: Record<string, any>) {
+    const { regions } = args
+
+    // @ts-expect-error
+    const key = getLayoutId(args)
+    const session = this.sessions[key]
+
+    if (session) {
+      const region = regions[0]!
+      session.layout.discardRange(region.refName, region.start, region.end)
+    }
   }
 
   async freeResourcesInClient(rpcManager: RpcManager, args: RenderArgs) {
     const { regions } = args
     const key = getLayoutId(args)
     const session = this.sessions[key]
+
     if (session) {
       const region = regions[0]!
       session.layout.discardRange(region.refName, region.start, region.end)
     }
-    return await super.freeResourcesInClient(rpcManager, args)
+    return super.freeResourcesInClient(rpcManager, args)
   }
 
   deserializeLayoutInClient(json: SerializedLayout) {
@@ -176,41 +123,42 @@ export default class BoxRendererType extends FeatureRendererType {
 
   createLayoutInWorker(args: RenderArgsDeserialized) {
     const { regions } = args
-    const session = this.getWorkerSession(args)
-    return session.layout.getSublayout(regions[0]!.refName)
+    const { layout } = this.getWorkerSession(args)
+    return layout.getSublayout(regions[0]!.refName)
   }
 
   serializeResultsInWorker(
     results: RenderResults,
     args: RenderArgsDeserialized,
   ): ResultsSerialized {
-    const serialized = super.serializeResultsInWorker(
+    const { features, ...rest } = super.serializeResultsInWorker(
       results,
       args,
     ) as ResultsSerialized
 
     const region = args.regions[0]!
-    serialized.layout = results.layout.serializeRegion(
+    const 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
+    return {
+      ...rest,
+      layout,
+      maxHeightReached: layout.maxHeightReached,
+      features: features.filter(f => !!layout.rectangles[f.uniqueId]),
+    }
   }
 
-  /**
-   * gets layout and renders
-   *
-   * @param props - render args
-   */
   async render(props: RenderArgsDeserialized): Promise<RenderResults> {
     const layout =
       (props.layout as undefined | BaseLayout<unknown>) ||
       this.createLayoutInWorker(props)
-    const result = await super.render({ ...props, layout })
-    return { ...result, layout }
+    const result = await super.render({
+      ...props,
+      layout,
+    })
+    return {
+      ...result,
+      layout,
+    }
   }
 }

packages/core/pluggableElementTypes/renderers/LayoutSession.ts

@@ -0,0 +1,77 @@
+import deepEqual from 'fast-deep-equal'
+
+import { readConfObject } from '../../configuration'
+import GranularRectLayout from '../../util/layouts/GranularRectLayout'
+import MultiLayout from '../../util/layouts/MultiLayout'
+
+import type { AnyConfigurationModel } from '../../configuration'
+import type SerializableFilterChain from './util/serializableFilterChain'
+
+export interface LayoutSessionProps {
+  config: AnyConfigurationModel
+  bpPerPx: number
+  filters?: SerializableFilterChain
+}
+
+export type MyMultiLayout = MultiLayout<GranularRectLayout<unknown>, unknown>
+
+export interface CachedLayout {
+  layout: MyMultiLayout
+  config: AnyConfigurationModel
+  filters?: SerializableFilterChain
+}
+
+export class LayoutSession implements LayoutSessionProps {
+  config: AnyConfigurationModel
+
+  bpPerPx: number
+
+  filters?: SerializableFilterChain
+
+  constructor(args: LayoutSessionProps) {
+    this.config = args.config
+    this.bpPerPx = args.bpPerPx
+    this.filters = args.filters
+  }
+
+  update(args: LayoutSessionProps) {
+    this.config = args.config
+    this.bpPerPx = args.bpPerPx
+    this.filters = args.filters
+    return this
+  }
+
+  makeLayout() {
+    return new MultiLayout(GranularRectLayout, {
+      maxHeight: readConfObject(this.config, 'maxHeight'),
+      displayMode: readConfObject(this.config, 'displayMode'),
+      pitchX: this.bpPerPx,
+      pitchY: readConfObject(this.config, 'noSpacing') ? 1 : 3,
+    })
+  }
+
+  /**
+   * @param layout -
+   * @returns true if the given layout is a valid one to use for this session
+   */
+  cachedLayoutIsValid(cachedLayout: CachedLayout) {
+    return (
+      cachedLayout.layout.subLayoutConstructorArgs.pitchX === this.bpPerPx &&
+      deepEqual(readConfObject(this.config), cachedLayout.config) &&
+      deepEqual(this.filters, cachedLayout.filters)
+    )
+  }
+
+  cachedLayout: CachedLayout | undefined
+
+  get layout(): MyMultiLayout {
+    if (!this.cachedLayout || !this.cachedLayoutIsValid(this.cachedLayout)) {
+      this.cachedLayout = {
+        layout: this.makeLayout(),
+        config: readConfObject(this.config),
+        filters: this.filters,
+      }
+    }
+    return this.cachedLayout.layout
+  }
+}

packages/core/pluggableElementTypes/renderers/ServerSideRendererType.tsx

@@ -202,14 +202,9 @@ export default class ServerSideRenderer extends RendererType {
 
   async freeResourcesInClient(rpcManager: RpcManager, args: RenderArgs) {
     const serializedArgs = this.serializeArgsInClient(args)
+    const { sessionId } = args
 
-    const freed = this.freeResources()
-    const freedRpc = (await rpcManager.call(
-      args.sessionId,
-      'CoreFreeResources',
-      serializedArgs,
-    )) as number
-    return freed + freedRpc
+    await rpcManager.call(sessionId, 'CoreFreeResources', serializedArgs)
   }
 }
 

packages/core/rpc/methods/CoreFreeResources.ts

@@ -10,21 +10,13 @@ import RpcMethodType from '../../pluggableElementTypes/RpcMethodType'
 export default class CoreFreeResources extends RpcMethodType {
   name = 'CoreFreeResources'
 
-  async execute(specification: Record<string, unknown>) {
-    let deleteCount = 0
-
-    deleteCount += freeAdapterResources(specification)
-
-    // pass the freeResources hint along to all the renderers as well
+  async execute(args: Record<string, unknown>) {
+    freeAdapterResources(args)
     this.pluginManager.getRendererTypes().forEach(renderer => {
-      const count = renderer.freeResources(/* specification */)
-      if (count) {
-        deleteCount += count
-      }
+      renderer.freeResources(args)
     })
-
-    return deleteCount
   }
+
   async serializeArguments(args: Record<string, unknown>, _rpcDriver: string) {
     return args
   }

plugins/alignments/src/PileupRenderer/PileupLayoutSession.ts

@@ -1,5 +1,5 @@
 import { readConfObject } from '@jbrowse/core/configuration'
-import { LayoutSession } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType'
+import { LayoutSession } from '@jbrowse/core/pluggableElementTypes/renderers/LayoutSession'
 import deepEqual from 'fast-deep-equal'
 
 import type { FilterBy, SortedBy } from '../shared/types'