@jbrowse/plugin-bed 2.3.1 → 2.3.3

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-bed",
-  "version": "2.3.1",
+  "version": "2.3.3",
   "description": "JBrowse 2 bed adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -38,7 +38,7 @@
   },
   "dependencies": {
     "@flatten-js/interval-tree": "^1.0.15",
-    "@gmod/bbi": "^2.0.3",
+    "@gmod/bbi": "^3.0.0",
     "@gmod/bed": "^2.1.2",
     "@gmod/bgzf-filehandle": "^1.4.3",
     "@gmod/tabix": "^1.5.2"
@@ -48,7 +48,7 @@
     "mobx": "^6.0.0",
     "mobx-react": "^7.0.0",
     "mobx-state-tree": "^5.0.0",
-    "rxjs": "^6.0.0"
+    "rxjs": "^7.0.0"
   },
   "publishConfig": {
     "access": "public"
@@ -56,5 +56,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "75c4cba2f50c626c62881abd5851dbf2435c2401"
+  "gitHead": "283e0387ccd5acc9f092cf00804d1fcac212e68d"
 }

package/src/BedAdapter/BedAdapter.test.ts

@@ -1,12 +1,8 @@
 import { toArray } from 'rxjs/operators'
+import { firstValueFrom } from 'rxjs'
 import BedAdapter from './BedAdapter'
 import MyConfigSchema from './configSchema'
 
-import { TextDecoder } from 'web-encoding'
-if (!window.TextDecoder) {
-  window.TextDecoder = TextDecoder
-}
-
 test('adapter can fetch features from volvox-bed12.bed', async () => {
   const adapter = new BedAdapter(
     MyConfigSchema.create({
@@ -26,7 +22,7 @@ test('adapter can fetch features from volvox-bed12.bed', async () => {
   expect(await adapter.hasDataForRefName('ctgA')).toBe(true)
   expect(await adapter.hasDataForRefName('ctgB')).toBe(false)
 
-  const featuresArray = await features.pipe(toArray()).toPromise()
+  const featuresArray = await firstValueFrom(features.pipe(toArray()))
   const featuresJsonArray = featuresArray.map(f => f.toJSON())
   expect(featuresJsonArray.slice(0, 10)).toMatchSnapshot()
 })
@@ -50,7 +46,7 @@ test('adapter can fetch features from volvox.sort.bed simple bed3', async () =>
   expect(await adapter.hasDataForRefName('contigA')).toBe(true)
   expect(await adapter.hasDataForRefName('ctgB')).toBe(false)
 
-  const featuresArray = await features.pipe(toArray()).toPromise()
+  const featuresArray = await firstValueFrom(features.pipe(toArray()))
   const featuresJsonArray = featuresArray.map(f => f.toJSON())
   expect(featuresJsonArray.slice(0, 10)).toMatchSnapshot()
 })
@@ -115,7 +111,7 @@ test('adapter can fetch features bed with autosql', async () => {
   expect(await adapter.hasDataForRefName('ctgA')).toBe(true)
   expect(await adapter.hasDataForRefName('ctgB')).toBe(false)
 
-  const featuresArray = await features.pipe(toArray()).toPromise()
+  const featuresArray = await firstValueFrom(features.pipe(toArray()))
   const featuresJsonArray = featuresArray.map(f => f.toJSON())
   expect(featuresJsonArray.slice(0, 10)).toMatchSnapshot()
 })
@@ -139,7 +135,7 @@ test('adapter can fetch bed with header', async () => {
   expect(await adapter.hasDataForRefName('contigA')).toBe(true)
   expect(await adapter.hasDataForRefName('ctgB')).toBe(false)
 
-  const featuresArray = await features.pipe(toArray()).toPromise()
+  const featuresArray = await firstValueFrom(features.pipe(toArray()))
   const featuresJsonArray = featuresArray.map(f => f.toJSON())
   expect(featuresJsonArray.slice(0, 10)).toMatchSnapshot()
 })
@@ -164,7 +160,7 @@ test('adapter can use gwas header', async () => {
     assemblyName: 'hg19',
   })
 
-  const featuresArray = await features.pipe(toArray()).toPromise()
+  const featuresArray = await firstValueFrom(features.pipe(toArray()))
   const featuresJsonArray = featuresArray.map(f => f.toJSON())
   expect(featuresJsonArray.slice(0, 10)).toMatchSnapshot()
 })

package/src/BedTabixAdapter/BedTabixAdapter.test.ts

@@ -1,4 +1,5 @@
 import { toArray } from 'rxjs/operators'
+import { firstValueFrom } from 'rxjs'
 import BedTabixAdapter from './BedTabixAdapter'
 import MyConfigSchema from './configSchema'
 
@@ -27,7 +28,7 @@ test('adapter can fetch features from volvox-bed12.bed.gz', async () => {
   expect(await adapter.hasDataForRefName('ctgA')).toBe(true)
   expect(await adapter.hasDataForRefName('ctgB')).toBe(false)
 
-  const featuresArray = await features.pipe(toArray()).toPromise()
+  const featuresArray = await firstValueFrom(features.pipe(toArray()))
   const featuresJsonArray = featuresArray.map(f => f.toJSON())
   expect(featuresJsonArray.slice(0, 10)).toMatchSnapshot()
 })
@@ -57,7 +58,7 @@ test('adapter can fetch features from volvox.sort.bed.gz simple bed3', async ()
   expect(await adapter.hasDataForRefName('contigA')).toBe(true)
   expect(await adapter.hasDataForRefName('ctgB')).toBe(false)
 
-  const featuresArray = await features.pipe(toArray()).toPromise()
+  const featuresArray = await firstValueFrom(features.pipe(toArray()))
   const featuresJsonArray = featuresArray.map(f => f.toJSON())
   expect(featuresJsonArray.slice(0, 10)).toMatchSnapshot()
 })
@@ -127,7 +128,7 @@ test('adapter can fetch features bed with autosql', async () => {
   expect(await adapter.hasDataForRefName('ctgA')).toBe(true)
   expect(await adapter.hasDataForRefName('ctgB')).toBe(false)
 
-  const featuresArray = await features.pipe(toArray()).toPromise()
+  const featuresArray = await firstValueFrom(features.pipe(toArray()))
   const featuresJsonArray = featuresArray.map(f => f.toJSON())
   expect(featuresJsonArray.slice(0, 10)).toMatchSnapshot()
 })
@@ -161,7 +162,7 @@ test('adapter can fetch bed with header', async () => {
   expect(await adapter.hasDataForRefName('contigA')).toBe(true)
   expect(await adapter.hasDataForRefName('ctgB')).toBe(false)
 
-  const featuresArray = await features.pipe(toArray()).toPromise()
+  const featuresArray = await firstValueFrom(features.pipe(toArray()))
   const featuresJsonArray = featuresArray.map(f => f.toJSON())
   expect(featuresJsonArray.slice(0, 10)).toMatchSnapshot()
 })
@@ -189,7 +190,7 @@ test('adapter can use gwas header', async () => {
     assemblyName: 'hg19',
   })
 
-  const featuresArray = await features.pipe(toArray()).toPromise()
+  const featuresArray = await firstValueFrom(features.pipe(toArray()))
   const featuresJsonArray = featuresArray.map(f => f.toJSON())
   expect(featuresJsonArray.slice(0, 10)).toMatchSnapshot()
 })

package/src/BigBedAdapter/BigBedAdapter.test.ts

@@ -1,4 +1,5 @@
 import { toArray } from 'rxjs/operators'
+import { firstValueFrom } from 'rxjs'
 import BigBedAdapter from './BigBedAdapter'
 import configSchema from './configSchema'
 
@@ -21,7 +22,7 @@ test('adapter can fetch features from volvox.bb', async () => {
   expect(await adapter.hasDataForRefName('ctgA')).toBe(true)
   expect(await adapter.hasDataForRefName('ctgB')).toBe(false)
 
-  const featuresArray = await features.pipe(toArray()).toPromise()
+  const featuresArray = await firstValueFrom(features.pipe(toArray()))
   const featuresJsonArray = featuresArray.map(f => f.toJSON())
   expect(featuresJsonArray).toMatchSnapshot()
 })

package/src/{index.test.js → index.test.ts}

@@ -3,7 +3,6 @@ import { getSnapshot } from 'mobx-state-tree'
 import ThisPlugin from '.'
 
 test('plugin in a stock JBrowse', () => {
-  console.warn = jest.fn()
   const pluginManager = new PluginManager([new ThisPlugin()])
   pluginManager.createPluggableElements()
   pluginManager.configure()