Merge origin/main

CHANGELOG.md

@@ -1,3 +1,52 @@
+yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.17.0
+
+## 2.17.0 (2024-11-18)
+
+#### :rocket: Enhancement
+
+- `core`
+  - [#4662](https://github.com/GMOD/jbrowse-components/pull/4662) Add better
+    handling for bedMethyl files ([@cmdcolin](https://github.com/cmdcolin))
+  - [#4652](https://github.com/GMOD/jbrowse-components/pull/4652) Reduce
+    re-rendering on quantitative and snpcoverage track height adjustments
+    ([@cmdcolin](https://github.com/cmdcolin))
+  - [#4651](https://github.com/GMOD/jbrowse-components/pull/4651) Add mismatches
+    cache to improve performance on ultra-long reads
+    ([@cmdcolin](https://github.com/cmdcolin))
+- Other
+  - [#4649](https://github.com/GMOD/jbrowse-components/pull/4649) Add support
+    for displaying SNPs in "no_ref" CRAM files
+    ([@cmdcolin](https://github.com/cmdcolin))
+  - [#4627](https://github.com/GMOD/jbrowse-components/pull/4627) Create BLAST
+    tabular adapter ([@garrettjstevens](https://github.com/garrettjstevens))
+
+#### :bug: Bug Fix
+
+- Other
+  - [#4647](https://github.com/GMOD/jbrowse-components/pull/4647) Improved
+    rendering of modifications ([@cmdcolin](https://github.com/cmdcolin))
+  - [#4646](https://github.com/GMOD/jbrowse-components/pull/4646) Fix mouseover
+    pixelation on linear synteny view ([@cmdcolin](https://github.com/cmdcolin))
+- `core`
+  - [#4639](https://github.com/GMOD/jbrowse-components/pull/4639) Fix RNA-seq
+    stranded arc coloring, change the color of RNA-seq introns, and improve
+    compact rendering ([@cmdcolin](https://github.com/cmdcolin))
+  - [#4638](https://github.com/GMOD/jbrowse-components/pull/4638) Fix rendering
+    of UCSC repeatmasker BigBed and BED files
+    ([@cmdcolin](https://github.com/cmdcolin))
+
+#### :house: Internal
+
+- `core`
+  - [#4648](https://github.com/GMOD/jbrowse-components/pull/4648) Run codemod
+    fix for some MUI deprecated props ([@cmdcolin](https://github.com/cmdcolin))
+
+#### Committers: 2
+
+- Colin Diesh ([@cmdcolin](https://github.com/cmdcolin))
+- Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) Done
+  in 1.81s.
+
 yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.16.1
 
 ## 2.16.1 (2024-11-03)

config/jest/url.js

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

eslint.config.mjs

@@ -130,6 +130,7 @@ export default tseslint.config(
       'unicorn/prefer-at': 'off',
       'unicorn/prefer-string-replace-all': 'off',
       'unicorn/no-array-reduce': 'off',
+      'unicorn/expiring-todo-comments': 'off',
 
       '@typescript-eslint/no-deprecated': 'off',
       '@typescript-eslint/no-explicit-any': 'off',

lerna.json

@@ -1,5 +1,5 @@
 {
-  "version": "2.16.1",
+  "version": "2.17.0",
   "npmClient": "yarn",
   "$schema": "node_modules/lerna/schemas/lerna-schema.json"
 }

packages/app-core/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/app-core",
-  "version": "2.16.1",
+  "version": "2.17.0",
   "description": "JBrowse 2 code shared between the 'full featured' apps e.g. jbrowse-web and jbrowse-desktop",
   "keywords": [
     "jbrowse",
@@ -42,7 +42,7 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.16.3",
-    "@jbrowse/product-core": "^2.16.1",
+    "@jbrowse/product-core": "^2.17.0",
     "@mui/icons-material": "^6.0.0",
     "@mui/material": "^6.0.0",
     "copy-to-clipboard": "^3.3.1"

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 {
@@ -253,4 +254,19 @@ export abstract class BaseFeatureDataAdapter extends BaseAdapter {
     }
     return this.getRegionFeatureDensityStats(regions[0]!, opts)
   }
+
+  async getSources(
+    regions: Region[],
+  ): Promise<{ name: string; color?: string; [key: string]: unknown }[]> {
+    const features = await firstValueFrom(
+      this.getFeaturesInMultipleRegions(regions).pipe(toArray()),
+    )
+    const sources = new Set<string>()
+    for (const f of features) {
+      sources.add(f.get('source'))
+    }
+    return [...sources].map(source => ({
+      name: source,
+    }))
+  }
 }

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/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "2.16.1",
+  "version": "2.17.0",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
     "jbrowse",

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(