@jbrowse/plugin-legacy-jbrowse 2.3.2 → 2.3.4

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-legacy-jbrowse",
-  "version": "2.3.2",
+  "version": "2.3.4",
   "description": "JBrowse 2 plugin for connecting to and reading JBrowse 1 data",
   "keywords": [
     "jbrowse",
@@ -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": "467d973535bb7b2664e9f66311fb0dc21c1ce5ba"
+  "gitHead": "98ae48be91ee2371e1b2768a907b4997995e9915"
 }

package/src/NCListAdapter/NCListAdapter.test.ts

@@ -1,8 +1,9 @@
 import { toArray } from 'rxjs/operators'
 import path from 'path'
+import { LocalFile, GenericFilehandle } from 'generic-filehandle'
+import { firstValueFrom } from 'rxjs'
 import Adapter from './NCListAdapter'
 import configSchema from './configSchema'
-import { LocalFile, GenericFilehandle } from 'generic-filehandle'
 
 export function generateReadBuffer(
   getFileFunction: (str: string) => GenericFilehandle,
@@ -42,12 +43,12 @@ test('adapter can fetch features from ensembl_genes test set', async () => {
     end: 35960388,
   })
 
-  const featuresArray = await features.pipe(toArray()).toPromise()
-  expect(featuresArray[0].get('refName')).toBe('21')
-  expect(featuresArray[0].id()).toBe(`test-21,0,0,19,22,0`)
-  const featuresJsonArray = featuresArray.map(f => f.toJSON())
-  expect(featuresJsonArray.length).toEqual(94)
-  for (const feature of featuresJsonArray) {
+  const featArr = await firstValueFrom(features.pipe(toArray()))
+  expect(featArr[0].get('refName')).toBe('21')
+  expect(featArr[0].id()).toBe(`test-21,0,0,19,22,0`)
+  const featJson = featArr.map(f => f.toJSON())
+  expect(featJson.length).toEqual(94)
+  for (const feature of featJson) {
     expect(feature).toMatchSnapshot({ uniqueId: expect.any(String) })
   }
 

package/src/index.test.ts

@@ -0,0 +1,35 @@
+import PluginManager from '@jbrowse/core/PluginManager'
+import { getSnapshot } from 'mobx-state-tree'
+import ThisPlugin from '.'
+
+test('plugin in a stock JBrowse', () => {
+  const pm = new PluginManager([new ThisPlugin()])
+  pm.createPluggableElements()
+  pm.configure()
+  expect(() => pm.addPlugin(new ThisPlugin())).toThrow(
+    /JBrowse already configured, cannot add plugins/,
+  )
+
+  const NCListAdapter = pm.getAdapterType('NCListAdapter')
+  const config = NCListAdapter.configSchema.create({ type: 'NCListAdapter' })
+  expect(getSnapshot(config)).toMatchSnapshot()
+})
+
+test('test creating a text search adapter', () => {
+  const pm = new PluginManager([new ThisPlugin()])
+  pm.createPluggableElements()
+  pm.configure()
+
+  const Adapter = pm.getTextSearchAdapterType('JBrowse1TextSearchAdapter')
+  const config = Adapter.configSchema.create({
+    type: 'JBrowse1TextSearchAdapter',
+    textSearchAdapterId: 'JBrowse1GenerateNamesAdapterTest',
+    namesIndexLocation: {
+      uri: 'names/',
+      locationType: 'UriLocation',
+    },
+    tracks: [],
+    assemblies: [],
+  })
+  expect(getSnapshot(config)).toMatchSnapshot()
+})

package/src/declare.d.ts

@@ -1 +0,0 @@
-declare module '@gmod/nclist'

package/src/index.test.js

@@ -1,41 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import { getSnapshot } from 'mobx-state-tree'
-import ThisPlugin from '.'
-
-test('plugin in a stock JBrowse', () => {
-  const originalConsoleWarn = console.warn
-  console.warn = jest.fn()
-  const pluginManager = new PluginManager([new ThisPlugin()])
-  pluginManager.createPluggableElements()
-  pluginManager.configure()
-  console.warn = originalConsoleWarn
-  expect(() => pluginManager.addPlugin(new ThisPlugin())).toThrow(
-    /JBrowse already configured, cannot add plugins/,
-  )
-
-  const NCListAdapter = pluginManager.getAdapterType('NCListAdapter')
-  const config = NCListAdapter.configSchema.create({ type: 'NCListAdapter' })
-  expect(getSnapshot(config)).toMatchSnapshot()
-})
-
-test('test creating a text search adapter', () => {
-  console.warn = jest.fn()
-  const pluginManager = new PluginManager([new ThisPlugin()])
-  pluginManager.createPluggableElements()
-  pluginManager.configure()
-
-  const JB1TextSearchAdapter = pluginManager.getTextSearchAdapterType(
-    'JBrowse1TextSearchAdapter',
-  )
-  const config = JB1TextSearchAdapter.configSchema.create({
-    type: 'JBrowse1TextSearchAdapter',
-    textSearchAdapterId: 'JBrowse1GenerateNamesAdapterTest',
-    namesIndexLocation: {
-      uri: 'names/',
-      locationType: 'UriLocation',
-    },
-    tracks: [],
-    assemblies: [],
-  })
-  expect(getSnapshot(config)).toMatchSnapshot()
-})