[skip ci] none

CHANGELOG.md

@@ -272,7 +272,7 @@ yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.13.1
   track selector in linear synteny view causing crash in v2.13.0
   ([@cmdcolin](https://github.com/cmdcolin))
 - [#4495](https://github.com/GMOD/jbrowse-components/pull/4495) Fix log scale
-  for some types of stopToken tracks ([@cmdcolin](https://github.com/cmdcolin))
+  for some types of signal tracks ([@cmdcolin](https://github.com/cmdcolin))
 
 #### Committers: 1
 
@@ -6437,7 +6437,7 @@ Broken releases missing some packages
     rendering outside it's allowed bounds
     ([@cmdcolin](https://github.com/cmdcolin))
   - [#1783](https://github.com/GMOD/jbrowse-components/pull/1783) Add hic
-    aborting and fix remoteAbort stopToken propagation
+    aborting and fix remoteAbort signal propagation
     ([@cmdcolin](https://github.com/cmdcolin))
   - [#1723](https://github.com/GMOD/jbrowse-components/pull/1723) A few bugfixes
     ([@garrettjstevens](https://github.com/garrettjstevens))

packages/core/assemblyManager/assembly.ts

@@ -62,7 +62,6 @@ async function loadRefNameMap(
 ) {
   const { sessionId } = options
   await when(() => !!(assembly.regions && assembly.refNameAliases), {
-    stopToken,
     name: 'when assembly ready',
   })
 
@@ -157,11 +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 => ({
@@ -175,6 +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
@@ -212,7 +231,7 @@ export default function assemblyFactory(
         return self.getConf('displayName')
       },
       /**
-       * #getter
+       * #method
        */
       hasName(name: string) {
         return this.allAliases.includes(name)

packages/core/util/when.ts

@@ -1,85 +1 @@
-import { when as mobxWhen, IWhenOptions } from 'mobx'
-import { checkStopToken } from './stopToken'
-
-interface WhenOpts extends IWhenOptions {
-  stopToken?: string
-}
-
-/**
- * Wrapper for mobx `when` that adds timeout and aborting support.
- */
-export function when(
-  getter: () => boolean,
-  { timeout, stopToken, name }: WhenOpts = {},
-) {
-  return new Promise((resolve, reject) => {
-    let finished = false
-
-    const whenPromise = mobxWhen(getter)
-
-    // set up timeout
-    let timeoutId: ReturnType<typeof setTimeout> | undefined
-    let finishTimeout = () => {}
-    if (timeout) {
-      timeoutId = setTimeout(() => {
-        if (!finished) {
-          finished = true
-          whenPromise.cancel()
-          reject(new Error(`timed out waiting for ${name || 'whenPresent'}`))
-        }
-      }, timeout)
-      finishTimeout = () => {
-        if (timeoutId) {
-          clearTimeout(timeoutId)
-        }
-      }
-    }
-
-    // set up aborting
-    if (stopToken !== undefined) {
-      try {
-        checkStopToken(stopToken)
-      } catch (e) {
-        finished = true
-        whenPromise.cancel()
-        finishTimeout()
-        reject(new Error('aborted'))
-      }
-    }
-
-    whenPromise
-      .then(() => {
-        if (!finished) {
-          finished = true
-          finishTimeout()
-
-          resolve(true)
-        }
-      })
-      .catch((err: unknown) => {
-        if (!finished) {
-          finished = true
-          finishTimeout()
-          // eslint-disable-next-line @typescript-eslint/prefer-promise-reject-errors
-          reject(err)
-        }
-      })
-  })
-}
-
-/**
- * Wrapper for mobx `when` that makes a promise for the return value
- * of the given function at the point in time when it becomes not
- * undefined and not null.
- */
-export async function whenPresent<FUNCTION extends () => unknown>(
-  getter: FUNCTION,
-  opts: WhenOpts = {},
-): Promise<NonNullable<ReturnType<FUNCTION>>> {
-  await when(() => {
-    const val = getter()
-    return val !== undefined && val !== null
-  }, opts)
-
-  return getter() as NonNullable<ReturnType<FUNCTION>>
-}
+export { when } from 'mobx'

plugins/bed/src/generateBedMethylFeature.ts

@@ -44,13 +44,14 @@ export function generateBedMethylFeature({
     n_diff,
     n_nocall,
   ] = line.split('\t')
+
   return {
     uniqueId,
     refName,
     start,
     end,
     code,
-    score: fraction_modified,
+    score: +fraction_modified! || 0,
     strand,
     color,
     source: code,

plugins/wiggle/src/getMultiWiggleSourcesAutorun.ts

@@ -1,14 +1,11 @@
 import { autorun } from 'mobx'
 import { addDisposer, isAlive } from 'mobx-state-tree'
 // jbrowse
-import {
-  getContainingView,
-  getSession,
-  isAbortException,
-} from '@jbrowse/core/util'
+import { getContainingView, getSession } from '@jbrowse/core/util'
 import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 import { AnyConfigurationModel } from '@jbrowse/core/configuration'
 import { getRpcSessionId } from '@jbrowse/core/util/tracks'
+import { isAbortException } from '@jbrowse/core/util/aborting'
 
 export interface Source {
   name: string
@@ -51,8 +48,8 @@ export function getMultiWiggleSourcesAutorun(self: {
           self.setSources(sources)
         }
       } catch (e) {
+        console.error(e)
         if (!isAbortException(e) && isAlive(self)) {
-          console.error(e)
           getSession(self).notifyError(`${e}`, e)
         }
       }

test_data/hs1/config.json

@@ -57,6 +57,19 @@
         }
       },
       "assemblyNames": ["hs1"]
+    },
+    {
+      "type": "FeatureTrack",
+      "trackId": "chm13v2.0_rmsk",
+      "name": "chm13v2.0_rmsk",
+      "adapter": {
+        "type": "BigBedAdapter",
+        "bigBedLocation": {
+          "uri": "https://hgdownload.soe.ucsc.edu/gbdb/hs1/t2tRepeatMasker/chm13v2.0_rmsk.bb",
+          "locationType": "UriLocation"
+        }
+      },
+      "assemblyNames": ["hs1"]
     }
   ]
 }