Replace AbortSignal with "stop token" to rescue some aborting behavior (

#4663)

config/jest/url.js

@@ -0,0 +1,2 @@
+URL.createObjectURL = () => `${Math.random()}`
+URL.revokeObjectURL = () => {}

packages/core/assemblyManager/assembly.ts

@@ -58,11 +58,10 @@ async function loadRefNameMap(
   assembly: Assembly,
   adapterConfig: unknown,
   options: BaseOptions,
-  signal?: AbortSignal,
+  stopToken?: string,
 ) {
   const { sessionId } = options
   await when(() => !!(assembly.regions && assembly.refNameAliases), {
-    signal,
     name: 'when assembly ready',
   })
 
@@ -71,7 +70,7 @@ async function loadRefNameMap(
     'CoreGetRefNames',
     {
       adapterConfig,
-      signal,
+      stopToken,
       ...options,
     },
     { timeout: 1000000 },
@@ -139,18 +138,14 @@ export default function assemblyFactory(
     cache: new QuickLRU({ maxSize: 1000 }),
 
     // @ts-expect-error
+    // TODO:ABORT (possible? desirable??)
     async fill(
       args: CacheData,
-      signal?: AbortSignal,
+      _stopToken?: string,
       statusCallback?: (arg: string) => void,
     ) {
       const { adapterConf, self, options } = args
-      return loadRefNameMap(
-        self,
-        adapterConf,
-        { ...options, statusCallback },
-        signal,
-      )
+      return loadRefNameMap(self, adapterConf, { ...options, statusCallback })
     },
   })
   return types
@@ -161,11 +156,29 @@ export default function assemblyFactory(
       configuration: types.safeReference(assemblyConfigType),
     })
     .volatile(() => ({
+      /**
+       * #volatile
+       */
       error: undefined as unknown,
+      /**
+       * #volatile
+       */
       loadingP: undefined as Promise<void> | undefined,
+      /**
+       * #volatile
+       */
       volatileRegions: undefined as BasicRegion[] | undefined,
+      /**
+       * #volatile
+       */
       refNameAliases: undefined as RefNameAliases | undefined,
+      /**
+       * #volatile
+       */
       lowerCaseRefNameAliases: undefined as RefNameAliases | undefined,
+      /**
+       * #volatile
+       */
       cytobands: undefined as Feature[] | undefined,
     }))
     .views(self => ({
@@ -179,6 +192,8 @@ export default function assemblyFactory(
     .views(self => ({
       /**
        * #getter
+       * this is a getter with a side effect of loading the data. not the best
+       * practice, but it helps to lazy load the assembly
        */
       get initialized() {
         // @ts-expect-error
@@ -216,7 +231,7 @@ export default function assemblyFactory(
         return self.getConf('displayName')
       },
       /**
-       * #getter
+       * #method
        */
       hasName(name: string) {
         return this.allAliases.includes(name)
@@ -453,7 +468,7 @@ export default function assemblyFactory(
        * #method
        */
       getAdapterMapEntry(adapterConf: AdapterConf, options: BaseOptions) {
-        const { signal, statusCallback, ...rest } = options
+        const { stopToken, statusCallback, ...rest } = options
         if (!options.sessionId) {
           throw new Error('sessionId is required')
         }
@@ -465,7 +480,7 @@ export default function assemblyFactory(
             options: rest,
           } as CacheData,
 
-          // signal intentionally not passed here, fixes issues like #2221.
+          // stopToken intentionally not passed here, fixes issues like #2221.
           // alternative fix #2540 was proposed but non-working currently
           undefined,
           statusCallback,
@@ -504,11 +519,11 @@ export default function assemblyFactory(
 async function getRefNameAliases({
   config,
   pluginManager,
-  signal,
+  stopToken,
 }: {
   config: AnyConfigurationModel
   pluginManager: PluginManager
-  signal?: AbortSignal
+  stopToken?: string
 }) {
   const type = pluginManager.getAdapterType(config.type)!
   const CLASS = await type.getAdapterClass()
@@ -517,7 +532,7 @@ async function getRefNameAliases({
     undefined,
     pluginManager,
   ) as BaseRefNameAliasAdapter
-  return adapter.getRefNameAliases({ signal })
+  return adapter.getRefNameAliases({ stopToken })
 }
 
 async function getCytobands({
@@ -538,16 +553,16 @@ async function getCytobands({
 async function getAssemblyRegions({
   config,
   pluginManager,
-  signal,
+  stopToken,
 }: {
   config: AnyConfigurationModel
   pluginManager: PluginManager
-  signal?: AbortSignal
+  stopToken?: string
 }) {
   const type = pluginManager.getAdapterType(config.type)!
   const CLASS = await type.getAdapterClass()
   const adapter = new CLASS(config, undefined, pluginManager) as RegionsAdapter
-  return adapter.getRegions({ signal })
+  return adapter.getRegions({ stopToken })
 }
 
 export type AssemblyModel = ReturnType<typeof assemblyFactory>

packages/core/assemblyManager/assemblyManager.ts

@@ -121,7 +121,7 @@ function assemblyManagerFactory(conf: IAnyType, pm: PluginManager) {
       async getRefNameMapForAdapter(
         adapterConf: AdapterConf,
         assemblyName: string | undefined,
-        opts: { signal?: AbortSignal; sessionId: string },
+        opts: { stopToken?: string; sessionId: string },
       ) {
         if (assemblyName) {
           const asm = await this.waitForAssembly(assemblyName)
@@ -136,7 +136,7 @@ function assemblyManagerFactory(conf: IAnyType, pm: PluginManager) {
       async getReverseRefNameMapForAdapter(
         adapterConf: AdapterConf,
         assemblyName: string | undefined,
-        opts: { signal?: AbortSignal; sessionId: string },
+        opts: { stopToken?: string; sessionId: string },
       ) {
         if (assemblyName) {
           const asm = await this.waitForAssembly(assemblyName)

packages/core/data_adapters/BaseAdapter/BaseFeatureDataAdapter.ts

@@ -6,10 +6,11 @@ import { BaseAdapter } from './BaseAdapter'
 import { BaseOptions } from './BaseOptions'
 import { FeatureDensityStats } from './types'
 import { ObservableCreate } from '../../util/rxjs'
-import { checkAbortSignal, sum, max, min } from '../../util'
+import { sum, max, min } from '../../util'
 import { Feature } from '../../util/simpleFeature'
 import { AugmentedRegion as Region } from '../../util/types'
 import { blankStats, rectifyStats, scoresToStats } from '../../util/stats'
+import { checkStopToken } from '../../util/stopToken'
 
 /**
  * Base class for feature adapters to extend. Defines some methods that
@@ -82,7 +83,7 @@ export abstract class BaseFeatureDataAdapter extends BaseAdapter {
   public getFeaturesInRegion(region: Region, opts: BaseOptions = {}) {
     return ObservableCreate<Feature>(async observer => {
       const hasData = await this.hasDataForRefName(region.refName, opts)
-      checkAbortSignal(opts.signal)
+      checkStopToken(opts.stopToken)
       if (!hasData) {
         observer.complete()
       } else {

packages/core/data_adapters/BaseAdapter/BaseOptions.ts

@@ -1,5 +1,5 @@
 export interface BaseOptions {
-  signal?: AbortSignal
+  stopToken?: string
   bpPerPx?: number
   sessionId?: string
   statusCallback?: (message: string) => void
@@ -12,7 +12,7 @@ export type SearchType = 'full' | 'prefix' | 'exact'
 export interface BaseTextSearchArgs {
   queryString: string
   searchType?: SearchType
-  signal?: AbortSignal
+  stopToken?: string
   limit?: number
   pageNumber?: number
 }

packages/core/data_adapters/BaseAdapter/types.ts

@@ -1,5 +1,5 @@
 export interface BaseOptions {
-  signal?: AbortSignal
+  stopToken?: string
   bpPerPx?: number
   sessionId?: string
   statusCallback?: (message: string) => void
@@ -12,7 +12,7 @@ export type SearchType = 'full' | 'prefix' | 'exact'
 export interface BaseTextSearchArgs {
   queryString: string
   searchType?: SearchType
-  signal?: AbortSignal
+  stopToken?: string
   limit?: number
   pageNumber?: number
 }

packages/core/pluggableElementTypes/RpcMethodType.test.ts

@@ -31,7 +31,7 @@ test('test serialize arguments with augmentLocationObject', async () => {
         testLocation: locationInAdapter,
       },
       filters: [],
-      signal: 'teststring',
+      stopToken: 'teststring',
       randomProperty: 'randomstring',
       parentObject: {
         nestedObject: {

packages/core/pluggableElementTypes/RpcMethodType.ts

@@ -10,16 +10,6 @@ import {
   UriLocation,
 } from '../util/types'
 
-import {
-  deserializeAbortSignal,
-  isRemoteAbortSignal,
-  RemoteAbortSignal,
-} from '../rpc/remoteAbortSignals'
-
-interface SerializedArgs {
-  signal?: RemoteAbortSignal
-  blobMap?: Record<string, File>
-}
 export type RpcMethodConstructor = new (pm: PluginManager) => RpcMethodType
 
 export default abstract class RpcMethodType extends PluggableElementBase {
@@ -58,21 +48,15 @@ export default abstract class RpcMethodType extends PluggableElementBase {
     return loc
   }
 
-  async deserializeArguments<T extends SerializedArgs>(
-    serializedArgs: T,
+  async deserializeArguments<T>(
+    args: T & { blobMap?: Record<string, File> },
     _rpcDriverClassName: string,
-  ) {
-    if (serializedArgs.blobMap) {
-      setBlobMap(serializedArgs.blobMap)
+  ): Promise<T> {
+    if (args.blobMap) {
+      setBlobMap(args.blobMap)
     }
-    const { signal } = serializedArgs
 
-    return {
-      ...serializedArgs,
-      signal: isRemoteAbortSignal(signal)
-        ? deserializeAbortSignal(signal)
-        : undefined,
-    }
+    return args
   }
 
   abstract execute(

packages/core/pluggableElementTypes/renderers/FeatureRendererType.ts

@@ -3,7 +3,7 @@ import clone from 'clone'
 import { firstValueFrom } from 'rxjs'
 
 // locals
-import { checkAbortSignal, iterMap } from '../../util'
+import { iterMap } from '../../util'
 import SimpleFeature, {
   Feature,
   SimpleFeatureSerialized,
@@ -20,6 +20,7 @@ import ServerSideRendererType, {
 } from './ServerSideRendererType'
 import { isFeatureAdapter } from '../../data_adapters/BaseAdapter'
 import { AnyConfigurationModel } from '../../configuration'
+import { checkStopToken } from '../../util/stopToken'
 
 export interface RenderArgs extends ServerSideRenderArgs {
   displayModel?: {
@@ -146,7 +147,7 @@ export default class FeatureRendererType extends ServerSideRendererType {
     renderArgs: RenderArgsDeserialized,
   ): Promise<Map<string, Feature>> {
     const pm = this.pluginManager
-    const { signal, regions, sessionId, adapterConfig } = renderArgs
+    const { stopToken, regions, sessionId, adapterConfig } = renderArgs
     const { dataAdapter } = await getAdapter(pm, sessionId, adapterConfig)
     if (!isFeatureAdapter(dataAdapter)) {
       throw new Error('Adapter does not support retrieving features')
@@ -176,7 +177,7 @@ export default class FeatureRendererType extends ServerSideRendererType {
         : dataAdapter.getFeaturesInMultipleRegions(requestRegions, renderArgs)
 
     const feats = await firstValueFrom(featureObservable.pipe(toArray()))
-    checkAbortSignal(signal)
+    checkStopToken(stopToken)
     return new Map<string, Feature>(
       feats
         .filter(feat => this.featurePassesFilters(renderArgs, feat))

packages/core/pluggableElementTypes/renderers/ServerSideRendererType.tsx

@@ -10,7 +10,7 @@ import {
 } from 'mobx-state-tree'
 
 // locals
-import { checkAbortSignal, getSerializedSvg, updateStatus } from '../../util'
+import { getSerializedSvg, updateStatus } from '../../util'
 import SerializableFilterChain, {
   SerializedFilterChain,
 } from './util/serializableFilterChain'
@@ -20,12 +20,13 @@ import { createJBrowseTheme } from '../../ui'
 
 import RendererType, { RenderProps, RenderResults } from './RendererType'
 import ServerSideRenderedContent from './ServerSideRenderedContent'
+import { checkStopToken } from '../../util/stopToken'
 
 interface BaseRenderArgs extends RenderProps {
   sessionId: string
-  // Note that signal serialization happens after serializeArgsInClient and
+  // Note that stopToken serialization happens after serializeArgsInClient and
   // deserialization happens before deserializeArgsInWorker
-  signal?: AbortSignal
+  stopToken?: string
   theme: ThemeOptions
   exportSVG?: {
     rasterizeLayers?: boolean
@@ -189,13 +190,13 @@ export default class ServerSideRenderer extends RendererType {
    * @param args - serialized render args
    */
   async renderInWorker(args: RenderArgsSerialized): Promise<ResultsSerialized> {
-    const { signal, statusCallback = () => {} } = args
+    const { stopToken, statusCallback = () => {} } = args
     const deserializedArgs = this.deserializeArgsInWorker(args)
 
     const results = await updateStatus('Rendering plot', statusCallback, () =>
       this.render(deserializedArgs),
     )
-    checkAbortSignal(signal)
+    checkStopToken(stopToken)
 
     // serialize the results for passing back to the main thread.
     // these will be transmitted to the main process, and will come out