Better autorun abort

GMOD · Nov 23, 2024 · 916bc11 · 916bc11
1 parent 18babc1
commit 916bc11
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Showing 3 changed files with 65 additions and 43 deletions.
diff --git a/plugins/gccontent/src/GCContentAdapter/GCContentAdapter.ts b/plugins/gccontent/src/GCContentAdapter/GCContentAdapter.ts
@@ -4,8 +4,14 @@ import {
 } from '@jbrowse/core/data_adapters/BaseAdapter'
 import { firstValueFrom } from 'rxjs'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
-import { SimpleFeature, Feature, Region } from '@jbrowse/core/util'
+import {
+  SimpleFeature,
+  Feature,
+  Region,
+  updateStatus,
+} from '@jbrowse/core/util'
 import { toArray } from 'rxjs/operators'
+import { checkStopToken } from '@jbrowse/core/util/stopToken'
 
 export default class GCContentAdapter extends BaseFeatureDataAdapter {
   private gcMode = 'content'
@@ -26,6 +32,7 @@ export default class GCContentAdapter extends BaseFeatureDataAdapter {
   }
 
   public getFeatures(query: Region, opts: BaseOptions) {
+    const { statusCallback = () => {}, stopToken } = opts || {}
     return ObservableCreate<Feature>(async observer => {
       const sequenceAdapter = await this.configure()
       const windowSize = this.getConf('windowSize')
@@ -42,50 +49,61 @@ export default class GCContentAdapter extends BaseFeatureDataAdapter {
         return
       }
 
-      const ret = sequenceAdapter.getFeatures(
-        {
-          ...query,
-          start: queryStart,
-          end: queryEnd,
-        },
-        opts,
+      const feats = await firstValueFrom(
+        sequenceAdapter
+          .getFeatures(
+            {
+              ...query,
+              start: queryStart,
+              end: queryEnd,
+            },
+            opts,
+          )
+          .pipe(toArray()),
       )
-      const feats = await firstValueFrom(ret.pipe(toArray()))
       const residues = feats[0]?.get('seq') || ''
 
-      for (let i = hw; i < residues.length - hw; i += windowDelta) {
-        const r = f ? residues[i] : residues.slice(i - hw, i + hw)
-        let nc = 0
-        let ng = 0
-        let len = 0
-        for (const letter of r) {
-          if (letter === 'c' || letter === 'C') {
-            nc++
-          } else if (letter === 'g' || letter === 'G') {
-            ng++
+      let start = performance.now()
+      await updateStatus('Calculating GC', statusCallback, () => {
+        for (let i = hw; i < residues.length - hw; i += windowDelta) {
+          if (performance.now() - start > 400) {
+            checkStopToken(stopToken)
+            start = performance.now()
           }
-          if (letter !== 'N') {
-            len++
+          const r = f ? residues[i] : residues.slice(i - hw, i + hw)
+          let nc = 0
+          let ng = 0
+          let len = 0
+          for (const letter of r) {
+            if (letter === 'c' || letter === 'C') {
+              nc++
+            } else if (letter === 'g' || letter === 'G') {
+              ng++
+            }
+            if (letter !== 'N') {
+              len++
+            }
           }
+          const pos = queryStart
+          const score =
+            this.gcMode === 'content'
+              ? (ng + nc) / (len || 1)
+              : this.gcMode === 'skew'
+                ? (ng - nc) / (ng + nc || 1)
+                : 0
+
+          observer.next(
+            new SimpleFeature({
+              uniqueId: `${this.id}_${pos + i}`,
+              refName: query.refName,
+              start: pos + i,
+              end: pos + i + windowDelta,
+              score,
+            }),
+          )
         }
-        const pos = queryStart
-        const score =
-          this.gcMode === 'content'
-            ? (ng + nc) / (len || 1)
-            : this.gcMode === 'skew'
-              ? (ng - nc) / (ng + nc || 1)
-              : 0
+      })
 
-        observer.next(
-          new SimpleFeature({
-            uniqueId: `${this.id}_${pos + i}`,
-            refName: query.refName,
-            start: pos + i,
-            end: pos + i + windowDelta,
-            score,
-          }),
-        )
-      }
       observer.complete()
     })
   }

diff --git a/plugins/wiggle/src/getQuantitativeStatsAutorun.ts b/plugins/wiggle/src/getQuantitativeStatsAutorun.ts
@@ -1,7 +1,7 @@
 import { autorun } from 'mobx'
 import { addDisposer, isAlive } from 'mobx-state-tree'
 // jbrowse
-import { getContainingView } from '@jbrowse/core/util'
+import { getContainingView, isAbortException } from '@jbrowse/core/util'
 import { QuantitativeStats } from '@jbrowse/core/util/stats'
 import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 import { AnyConfigurationModel } from '@jbrowse/core/configuration'
@@ -44,8 +44,8 @@ export function getQuantitativeStatsAutorun(self: {
             }
           }
         } catch (e) {
-          console.error(e)
-          if (isAlive(self)) {
+          if (isAlive(self) && !isAbortException(e)) {
+            console.error(e)
             self.setError(e)
           }
         }

diff --git a/plugins/wiggle/src/shared/SharedWiggleMixin.ts b/plugins/wiggle/src/shared/SharedWiggleMixin.ts
@@ -16,6 +16,7 @@ import { types } from 'mobx-state-tree'
 // locals
 import { getNiceDomain } from '../util'
 import { lazy } from 'react'
+import { stopStopToken } from '@jbrowse/core/util/stopToken'
 
 // lazies
 const SetMinMaxDialog = lazy(() => import('./SetMinMaxDialog'))
@@ -155,8 +156,11 @@ export default function SharedWiggleMixin(
       /**
        * #action
        */
-      setStatsLoading() {
-        /* do nothing */
+      setStatsLoading(arg?: string) {
+        if (self.statsFetchInProgress) {
+          stopStopToken(self.statsFetchInProgress)
+        }
+        self.statsFetchInProgress = arg
       },
 
       /**