@jbrowse/plugin-wiggle 1.4.1 → 1.5.2

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-wiggle",
-  "version": "1.4.1",
+  "version": "1.5.2",
   "description": "JBrowse 2 wiggle adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -35,7 +35,7 @@
     "useSrc": "node ../../scripts/useSrc.js"
   },
   "dependencies": {
-    "@gmod/bbi": "^1.0.30",
+    "@gmod/bbi": "^1.0.31",
     "@material-ui/icons": "^4.11.2",
     "@popperjs/core": "^2.9.3",
     "abortable-promise-cache": "^1.1.3",
@@ -60,5 +60,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "42c7e1b98bb0d16fa440a8a8f500a1030607f16c"
+  "gitHead": "94fdfbc34787ab8f12a87e00038da74b247b42fa"
 }

package/src/BigWigAdapter/BigWigAdapter.test.ts

@@ -7,7 +7,10 @@ describe('adapter can fetch features from volvox.bw', () => {
   beforeEach(() => {
     adapter = new BigWigAdapter(
       configSchema.create({
-        bigWigLocation: { localPath: require.resolve('./test_data/volvox.bw') },
+        bigWigLocation: {
+          localPath: require.resolve('./test_data/volvox.bw'),
+          locationType: 'LocalPathLocation',
+        },
       }),
     )
   })
@@ -16,6 +19,7 @@ describe('adapter can fetch features from volvox.bw', () => {
       refName: 'ctgA',
       start: 0,
       end: 20000,
+      assemblyName: 'volvox',
     })
     expect(await adapter.refIdToName(0)).toBe('ctgA')
     expect(await adapter.refIdToName(1)).toBe(undefined)

package/src/BigWigAdapter/BigWigAdapter.ts

@@ -1,9 +1,9 @@
-import { BigWig, Feature as BBIFeature } from '@gmod/bbi'
+import { BigWig } from '@gmod/bbi'
 import {
   BaseFeatureDataAdapter,
   BaseOptions,
 } from '@jbrowse/core/data_adapters/BaseAdapter'
-import { NoAssemblyRegion } from '@jbrowse/core/util/types'
+import { AugmentedRegion as Region } from '@jbrowse/core/util/types'
 import { openLocation } from '@jbrowse/core/util/io'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
 import SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'
@@ -11,8 +11,10 @@ import { map, mergeAll } from 'rxjs/operators'
 import { readConfObject } from '@jbrowse/core/configuration'
 import { Instance } from 'mobx-state-tree'
 import { rectifyStats, UnrectifiedFeatureStats } from '@jbrowse/core/util/stats'
+import PluginManager from '@jbrowse/core/PluginManager'
 
 import configSchema from './configSchema'
+import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
 
 interface WiggleOptions extends BaseOptions {
   resolution?: number
@@ -27,10 +29,17 @@ export default class BigWigAdapter extends BaseFeatureDataAdapter {
     'hasGlobalStats',
   ]
 
-  public constructor(config: Instance<typeof configSchema>) {
-    super(config)
+  public constructor(
+    config: Instance<typeof configSchema>,
+    getSubAdapter?: getSubAdapterType,
+    pluginManager?: PluginManager,
+  ) {
+    super(config, getSubAdapter, pluginManager)
     this.bigwig = new BigWig({
-      filehandle: openLocation(readConfObject(config, 'bigWigLocation')),
+      filehandle: openLocation(
+        readConfObject(config, 'bigWigLocation'),
+        this.pluginManager,
+      ),
     })
   }
 
@@ -57,7 +66,7 @@ export default class BigWigAdapter extends BaseFeatureDataAdapter {
     return rectifyStats(header.totalSummary as UnrectifiedFeatureStats)
   }
 
-  public getFeatures(region: NoAssemblyRegion, opts: WiggleOptions = {}) {
+  public getFeatures(region: Region, opts: WiggleOptions = {}) {
     const { refName, start, end } = region
     const {
       bpPerPx = 0,
@@ -73,7 +82,7 @@ export default class BigWigAdapter extends BaseFeatureDataAdapter {
       })
       ob.pipe(
         mergeAll(),
-        map((record: BBIFeature) => {
+        map(record => {
           return new SimpleFeature({
             id: `${refName}:${record.start}-${record.end}`,
             data: { ...record, refName },
@@ -85,5 +94,3 @@ export default class BigWigAdapter extends BaseFeatureDataAdapter {
 
   public freeResources(): void {}
 }
-const adapterCapabilities = BigWigAdapter.capabilities
-export { adapterCapabilities }

package/src/BigWigAdapter/configSchema.ts

@@ -5,7 +5,10 @@ export default ConfigurationSchema(
   {
     bigWigLocation: {
       type: 'fileLocation',
-      defaultValue: { uri: '/path/to/my.bw' },
+      defaultValue: {
+        uri: '/path/to/my.bw',
+        locationType: 'UriLocation',
+      },
     },
   },
   { explicitlyTyped: true },

package/src/BigWigAdapter/index.ts

@@ -1,2 +1 @@
 export { default as configSchema } from './configSchema'
-export { adapterCapabilities } from './BigWigAdapter'

package/src/LinearWiggleDisplay/components/Tooltip.tsx

@@ -1,8 +1,9 @@
-/* eslint-disable @typescript-eslint/no-explicit-any */
 import React, { useMemo, useState } from 'react'
 import { observer } from 'mobx-react'
 import { makeStyles, alpha, Portal } from '@material-ui/core'
 import { Feature } from '@jbrowse/core/util/simpleFeature'
+
+// locals
 import { YSCALEBAR_LABEL_OFFSET } from '../models/model'
 import { usePopper } from 'react-popper'
 
@@ -86,18 +87,19 @@ const Tooltip = observer(
     clientRect,
     TooltipContents,
   }: {
-    model: any
+    model: { featureUnderMouse: Feature }
     height: number
     clientMouseCoord: Coord
     offsetMouseCoord: Coord
     clientRect?: ClientRect
+
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     TooltipContents: React.FC<any>
   }) => {
     const { featureUnderMouse } = model
-    const classes = useStyles()
     const [width, setWidth] = useState(0)
-
-    const [popperElement, setPopperElement] = useState<any>(null)
+    const [anchorEl, setAnchorEl] = useState<HTMLDivElement | null>(null)
+    const classes = useStyles()
 
     // must be memoized a la https://github.com/popperjs/react-popper/issues/391
     const virtElement = useMemo(
@@ -112,18 +114,21 @@ const Tooltip = observer(
             right: x,
             width: 0,
             height: 0,
+            x,
+            y,
+            toJSON() {},
           }
         },
       }),
       [clientRect?.top, clientMouseCoord, width],
     )
-    const { styles, attributes } = usePopper(virtElement, popperElement)
+    const { styles, attributes } = usePopper(virtElement, anchorEl)
 
     return featureUnderMouse ? (
       <>
         <Portal>
           <div
-            ref={setPopperElement}
+            ref={setAnchorEl}
             className={classes.tooltip}
             // zIndex needed to go over widget drawer
             style={{ ...styles.popper, zIndex: 100000 }}
@@ -152,7 +157,7 @@ const Tooltip = observer(
 
 const WiggleTooltip = observer(
   (props: {
-    model: any
+    model: { featureUnderMouse: Feature }
     height: number
     offsetMouseCoord: Coord
     clientMouseCoord: Coord

package/src/LinearWiggleDisplay/models/configSchema.ts

@@ -4,15 +4,12 @@ import { types } from 'mobx-state-tree'
 import PluginManager from '@jbrowse/core/PluginManager'
 
 export default function WiggleConfigFactory(pluginManager: PluginManager) {
-  const XYPlotRendererConfigSchema = pluginManager.getRendererType(
-    'XYPlotRenderer',
-  ).configSchema
-  const DensityRendererConfigSchema = pluginManager.getRendererType(
-    'DensityRenderer',
-  ).configSchema
-  const LinePlotRendererConfigSchema = pluginManager.getRendererType(
-    'LinePlotRenderer',
-  ).configSchema
+  const XYPlotRendererConfigSchema =
+    pluginManager.getRendererType('XYPlotRenderer').configSchema
+  const DensityRendererConfigSchema =
+    pluginManager.getRendererType('DensityRenderer').configSchema
+  const LinePlotRendererConfigSchema =
+    pluginManager.getRendererType('LinePlotRenderer').configSchema
 
   return ConfigurationSchema(
     'LinearWiggleDisplay',

package/src/LinearWiggleDisplay/models/model.tsx

@@ -162,7 +162,7 @@ const stateModelFactory = (
     }))
     .views(self => ({
       get TooltipComponent(): React.FC {
-        return (Tooltip as unknown) as React.FC
+        return Tooltip as unknown as React.FC
       },
 
       get adapterTypeName() {
@@ -438,17 +438,19 @@ const stateModelFactory = (
             {
               label: 'Set min/max score',
               onClick: () => {
-                getSession(self).setDialogComponent(SetMinMaxDlg, {
-                  model: self,
-                })
+                getSession(self).queueDialog((doneCallback: Function) => [
+                  SetMinMaxDlg,
+                  { model: self, handleClose: doneCallback },
+                ])
               },
             },
             {
               label: 'Set color',
               onClick: () => {
-                getSession(self).setDialogComponent(SetColorDlg, {
-                  model: self,
-                })
+                getSession(self).queueDialog((doneCallback: Function) => [
+                  SetColorDlg,
+                  { model: self, handleClose: doneCallback },
+                ])
               },
             },
           ]
@@ -507,7 +509,7 @@ const stateModelFactory = (
               regions: dynamicBlocks.contentBlocks.map(region => {
                 const { start, end } = region
                 return {
-                  ...region,
+                  ...JSON.parse(JSON.stringify(region)),
                   start: Math.floor(start),
                   end: Math.ceil(end),
                 }
@@ -542,13 +544,18 @@ const stateModelFactory = (
         async reload() {
           self.setError()
           const aborter = new AbortController()
-          const stats = await getStats({
-            signal: aborter.signal,
-            filters: self.filters,
-          })
-          if (isAlive(self)) {
-            self.updateStats(stats)
-            superReload()
+          let stats
+          try {
+            stats = await getStats({
+              signal: aborter.signal,
+              filters: self.filters,
+            })
+            if (isAlive(self)) {
+              self.updateStats(stats)
+              superReload()
+            }
+          } catch (e) {
+            self.setError(e)
           }
         },
         afterAttach() {
@@ -579,6 +586,7 @@ const stateModelFactory = (
                   }
                 } catch (e) {
                   if (!isAbortException(e) && isAlive(self)) {
+                    console.error(e)
                     self.setError(e)
                   }
                 }

package/src/WiggleRPC/rpcMethods.ts

@@ -74,17 +74,20 @@ export class WiggleGetMultiRegionStats extends RpcMethodType {
 
   async serializeArguments(
     args: RenderArgs & { signal?: AbortSignal; statusCallback?: Function },
+    rpcDriverClassName: string,
   ) {
-    const assemblyManager = this.pluginManager.rootModel?.session
-      ?.assemblyManager
+    const assemblyManager =
+      this.pluginManager.rootModel?.session?.assemblyManager
     if (!assemblyManager) {
       return args
     }
 
-    return renameRegionsIfNeeded(assemblyManager, {
+    const renamedArgs = await renameRegionsIfNeeded(assemblyManager, {
       ...args,
       filters: args.filters && args.filters.toJSON().filters,
     })
+
+    return super.serializeArguments(renamedArgs, rpcDriverClassName)
   }
 
   async execute(

package/src/WiggleRendering.tsx

@@ -14,6 +14,7 @@ function WiggleRendering(props: {
   onMouseLeave: Function
   onMouseMove: Function
   onFeatureClick: Function
+  blockKey: string
 }) {
   const {
     regions,

package/src/XYPlotRenderer/XYPlotRenderer.ts

@@ -43,7 +43,7 @@ export default class XYPlotRenderer extends WiggleBaseRenderer {
     const originY = getOrigin(scaleOpts.scaleType)
     const [niceMin, niceMax] = scale.domain()
 
-    const toY = (n: number) => height - scale(n) + offset
+    const toY = (n: number) => height - (scale(n) || 0) + offset
     const toHeight = (n: number) => toY(originY) - toY(n)
 
     const colorCallback =

package/src/index.ts

@@ -9,12 +9,10 @@ import {
   createBaseTrackModel,
 } from '@jbrowse/core/pluggableElementTypes/models'
 import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'
+import { FileLocation } from '@jbrowse/core/util/types'
 import WiggleBaseRenderer from './WiggleBaseRenderer'
 import WiggleRendering from './WiggleRendering'
-import {
-  configSchema as bigWigAdapterConfigSchema,
-  adapterCapabilities,
-} from './BigWigAdapter'
+import { configSchema as bigWigAdapterConfigSchema } from './BigWigAdapter'
 import DensityRenderer, {
   configSchema as densityRendererConfigSchema,
   ReactComponent as DensityRendererReactComponent,
@@ -38,6 +36,11 @@ import {
   WiggleGetGlobalStats,
   WiggleGetMultiRegionStats,
 } from './WiggleRPC/rpcMethods'
+import {
+  AdapterGuesser,
+  getFileName,
+  TrackTypeGuesser,
+} from '@jbrowse/core/util/tracks'
 
 export default class WigglePlugin extends Plugin {
   name = 'WigglePlugin'
@@ -80,11 +83,47 @@ export default class WigglePlugin extends Plugin {
         new AdapterType({
           name: 'BigWigAdapter',
           configSchema: bigWigAdapterConfigSchema,
-          adapterCapabilities,
+          adapterCapabilities: [
+            'hasResolution',
+            'hasLocalStats',
+            'hasGlobalStats',
+          ],
           getAdapterClass: () =>
             import('./BigWigAdapter/BigWigAdapter').then(r => r.default),
         }),
     )
+    pluginManager.addToExtensionPoint(
+      'Core-guessAdapterForLocation',
+      (adapterGuesser: AdapterGuesser) => {
+        return (
+          file: FileLocation,
+          index?: FileLocation,
+          adapterHint?: string,
+        ) => {
+          const regexGuess = /\.(bw|bigwig)$/i
+          const adapterName = 'BigWigAdapter'
+          const fileName = getFileName(file)
+          if (regexGuess.test(fileName) || adapterHint === adapterName) {
+            return {
+              type: adapterName,
+              bigWigLocation: file,
+            }
+          }
+          return adapterGuesser(file, index, adapterHint)
+        }
+      },
+    )
+    pluginManager.addToExtensionPoint(
+      'Core-guessTrackTypeForLocation',
+      (trackTypeGuesser: TrackTypeGuesser) => {
+        return (adapterName: string) => {
+          if (adapterName === 'BigWigAdapter') {
+            return 'QuantitativeTrack'
+          }
+          return trackTypeGuesser(adapterName)
+        }
+      },
+    )
 
     pluginManager.addRendererType(
       () =>