@jbrowse/plugin-data-management 2.3.2 → 2.3.3

package/esm/ucsc-trackhub/index.js

@@ -1,3 +1,14 @@
-export { default as modelFactory } from './model';
-export { default as configSchema } from './configSchema';
+import { ConnectionType } from '@jbrowse/core/pluggableElementTypes';
+import stateModelFactory from './model';
+import configSchema from './configSchema';
+export default (pluginManager) => {
+    pluginManager.addConnectionType(() => new ConnectionType({
+        name: 'UCSCTrackHubConnection',
+        configSchema,
+        stateModel: stateModelFactory(pluginManager),
+        displayName: 'UCSC Track Hub',
+        description: 'A track or assembly hub in the Track Hub format',
+        url: '//genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Intro',
+    }));
+};
 //# sourceMappingURL=index.js.map

package/esm/ucsc-trackhub/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/ucsc-trackhub/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,SAAS,CAAA;AACjD,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,gBAAgB,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/ucsc-trackhub/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,cAAc,EAAE,MAAM,qCAAqC,CAAA;AAGpE,OAAO,iBAAiB,MAAM,SAAS,CAAA;AACvC,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,iBAAiB,CAC7B,GAAG,EAAE,CACH,IAAI,cAAc,CAAC;QACjB,IAAI,EAAE,wBAAwB;QAC9B,YAAY;QACZ,UAAU,EAAE,iBAAiB,CAAC,aAAa,CAAC;QAC5C,WAAW,EAAE,gBAAgB;QAC7B,WAAW,EAAE,iDAAiD;QAC9D,GAAG,EAAE,6DAA6D;KACnE,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-data-management",
-  "version": "2.3.2",
+  "version": "2.3.3",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",
@@ -60,5 +60,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "467d973535bb7b2664e9f66311fb0dc21c1ce5ba"
+  "gitHead": "283e0387ccd5acc9f092cf00804d1fcac212e68d"
 }

package/src/AddConnectionWidget/components/{AddConnectionWidget.test.js → AddConnectionWidget.test.tsx}

@@ -1,14 +1,18 @@
-import { render, cleanup, fireEvent } from '@testing-library/react'
 import React from 'react'
+import { render, cleanup, fireEvent } from '@testing-library/react'
 import { createTestSession } from '@jbrowse/web/src/rootModel'
+
+// locals
 import AddConnectionWidget from './AddConnectionWidget'
+
 jest.mock('@jbrowse/web/src/makeWorkerInstance', () => () => {})
 
-window.fetch = jest.fn(() => new Promise(resolve => resolve()))
+// window.fetch = jest.fn(() => new Promise(resolve => resolve()))
 
 describe('<AddConnectionWidget />', () => {
-  let model
-  let session
+  // eslint-disable-next-line @typescript-eslint/no-explicit-any
+  let model: any
+  let session: ReturnType<typeof createTestSession>
 
   beforeEach(() => {
     session = createTestSession()
@@ -42,7 +46,8 @@ describe('<AddConnectionWidget />', () => {
   })
 
   it('can handle a custom UCSC trackHub URL', async () => {
-    const mockFetch = url => {
+    const mockFetch = async (url: RequestInfo | URL) => {
+      // @ts-ignore
       const urlText = url.href ? url.href : url
       let responseText = ''
       if (urlText.endsWith('hub.txt')) {
@@ -66,9 +71,11 @@ type bigWig
 `
       }
 
-      return Promise.resolve(new Response(responseText, { url: urlText }))
+      return new Response(responseText)
     }
+
     jest.spyOn(global, 'fetch').mockImplementation(mockFetch)
+
     const { findByTestId, getAllByRole, findAllByText, findByDisplayValue } =
       render(<AddConnectionWidget model={model} />)
     expect(session.connections.length).toBe(0)
@@ -90,7 +97,8 @@ type bigWig
   })
 
   it('can handle a custom JBrowse 1 data directory URL', async () => {
-    const mockFetch = url => {
+    const mockFetch = async (url: RequestInfo | URL) => {
+      // @ts-ignore
       const urlText = url.href ? url.href : url
       let responseText = ''
       if (urlText.endsWith('trackList.json')) {
@@ -98,9 +106,10 @@ type bigWig
       } else if (urlText.endsWith('refSeqs.json')) {
         responseText = '[]'
       }
-      return Promise.resolve(new Response(responseText, { url: urlText }))
+      return new Response(responseText)
     }
     jest.spyOn(global, 'fetch').mockImplementation(mockFetch)
+
     const {
       findByTestId,
       getAllByRole,

package/src/AddConnectionWidget/index.ts

@@ -1,4 +1,19 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
+import { WidgetType } from '@jbrowse/core/pluggableElementTypes'
+import PluginManager from '@jbrowse/core/PluginManager'
+import { lazy } from 'react'
 
-export { default as stateModel } from './model'
-export const configSchema = ConfigurationSchema('AddConnectionWidget', {})
+import stateModel from './model'
+const configSchema = ConfigurationSchema('AddConnectionWidget', {})
+
+export default (pluginManager: PluginManager) => {
+  pluginManager.addWidgetType(() => {
+    return new WidgetType({
+      name: 'AddConnectionWidget',
+      heading: 'Add a connection',
+      configSchema,
+      stateModel,
+      ReactComponent: lazy(() => import('./components/AddConnectionWidget')),
+    })
+  })
+}

package/src/AddTrackWidget/{index.test.jsx → index.test.tsx}

@@ -52,10 +52,13 @@ function standardInitializer() {
 const realLocation = window.location
 
 // https://stackoverflow.com/a/60110508/2129219
-function setWindowLoc(loc) {
+function setWindowLoc(loc: string) {
+  // @ts-ignore
   delete window.location
+  // @ts-ignore
   window.location = new URL(loc)
 }
+
 const FakeViewModel = types.model('FakeView', {
   id: types.identifier,
   type: types.literal('FakeView'),
@@ -67,7 +70,7 @@ const FakeViewModel = types.model('FakeView', {
 class FakeViewPlugin extends Plugin {
   name = 'FakeViewPlugin'
 
-  install(pluginManager) {
+  install(pluginManager: PluginManager) {
     pluginManager.addViewType(() => {
       return new ViewType({
         name: 'FakeView',
@@ -79,7 +82,7 @@ class FakeViewPlugin extends Plugin {
 }
 
 describe('tests on an LGV type system with view.assemblyNames, using URL', () => {
-  let session
+  let session: ReturnType<typeof standardInitializer>
   beforeEach(() => {
     session = standardInitializer()
   })
@@ -89,7 +92,6 @@ describe('tests on an LGV type system with view.assemblyNames, using URL', () =>
   })
 
   it('adds relative URL (BAM)', () => {
-    console.warn = jest.fn()
     const { widget } = session
     widget.setTrackData({
       uri: 'volvox-sorted.bam',
@@ -135,45 +137,40 @@ describe('tests on an LGV type system with view.assemblyNames, using URL', () =>
   })
 })
 
-describe('tests on an view without view.assemblyNames', () => {
-  let session
-  beforeEach(() => {
-    const pluginManager = new PluginManager([new FakeViewPlugin()])
-    pluginManager.createPluggableElements()
-    pluginManager.configure()
-    const SessionModel = types.model({
-      view: FakeViewModel,
-      widget: stateModelFactory(pluginManager),
-    })
+test('tests on an view without view.assemblyNames', () => {
+  const pluginManager = new PluginManager([new FakeViewPlugin()])
+  pluginManager.createPluggableElements()
+  pluginManager.configure()
 
-    // no assemblyNames on the view, just in case some view does not implement
-    // view.assemblyNames (it is just a convenience)
-    session = SessionModel.create({
-      view: {
-        type: 'FakeView',
-        id: 'testing',
-      },
-      widget: {
-        type: 'AddTrackWidget',
-        view: 'testing',
-      },
-    })
+  const SessionModel = types.model({
+    view: FakeViewModel,
+    widget: stateModelFactory(pluginManager),
+  })
+  // no assemblyNames on the view, just in case some view does not implement
+  // view.assemblyNames (it is just a convenience)
+  const session = SessionModel.create({
+    view: {
+      type: 'FakeView',
+      id: 'testing',
+    },
+    widget: {
+      type: 'AddTrackWidget',
+      view: 'testing',
+    },
   })
 
-  it('adds url', () => {
-    const { widget } = session
-    widget.setTrackData({
-      uri: 'volvox-sorted.bam',
-      locationType: 'UriLocation',
-    })
-    expect(widget.trackName).toBe('volvox-sorted.bam')
-    expect(widget.isRelativeUrl).toBe(true)
-    expect(widget.assembly).toBe(undefined)
+  const { widget } = session
+  widget.setTrackData({
+    uri: 'volvox-sorted.bam',
+    locationType: 'UriLocation',
   })
+  expect(widget.trackName).toBe('volvox-sorted.bam')
+  expect(widget.isRelativeUrl).toBe(true)
+  expect(widget.assembly).toBe(undefined)
 })
 
 describe('tests different file types', () => {
-  let session
+  let session: ReturnType<typeof standardInitializer>
   beforeEach(() => {
     session = standardInitializer()
   })
@@ -229,7 +226,7 @@ describe('tests different file types', () => {
 })
 
 describe('tests localpath', () => {
-  let session
+  let session: ReturnType<typeof standardInitializer>
   beforeEach(() => {
     session = standardInitializer()
   })

package/src/AddTrackWidget/index.ts

@@ -1,4 +1,19 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
+import { WidgetType } from '@jbrowse/core/pluggableElementTypes'
+import PluginManager from '@jbrowse/core/PluginManager'
+import { lazy } from 'react'
 
-export { default as stateModelFactory } from './model'
-export const configSchema = ConfigurationSchema('AddTrackWidget', {})
+import stateModelFactory from './model'
+const configSchema = ConfigurationSchema('AddTrackWidget', {})
+
+export default (pluginManager: PluginManager) => {
+  pluginManager.addWidgetType(() => {
+    return new WidgetType({
+      name: 'AddTrackWidget',
+      heading: 'Add a track',
+      configSchema,
+      stateModel: stateModelFactory(pluginManager),
+      ReactComponent: lazy(() => import('./components/AddTrackWidget')),
+    })
+  })
+}

package/src/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.test.tsx

@@ -1,7 +1,7 @@
 import React from 'react'
 import { createJBrowseTheme } from '@jbrowse/core/ui'
 import { createTestSession } from '@jbrowse/web/src/rootModel'
-import { cleanup, render } from '@testing-library/react'
+import { render } from '@testing-library/react'
 import { ThemeProvider } from '@mui/material/styles'
 
 // locals
@@ -13,140 +13,136 @@ jest.mock('@jbrowse/web/src/makeWorkerInstance', () => () => {})
 window.requestIdleCallback = cb => cb()
 window.cancelIdleCallback = () => {}
 
-describe('HierarchicalTrackSelector widget', () => {
-  afterEach(cleanup)
+test('renders nothing with no assembly', () => {
+  const session = createTestSession()
+  const firstView = session.addView('LinearGenomeView')
+  const model = firstView.activateTrackSelector()
 
-  it('renders nothing with no assembly', () => {
-    const session = createTestSession()
-    const firstView = session.addView('LinearGenomeView')
-    const model = firstView.activateTrackSelector()
+  const { container } = render(
+    <ThemeProvider theme={createJBrowseTheme()}>
+      {/* @ts-ignore*/}
+      <HierarchicalTrackSelector model={model} />
+    </ThemeProvider>,
+  )
+  expect(container.firstChild).toMatchSnapshot()
+})
 
-    const { container } = render(
-      <ThemeProvider theme={createJBrowseTheme()}>
-        {/* @ts-ignore*/}
-        <HierarchicalTrackSelector model={model} />
-      </ThemeProvider>,
-    )
-    expect(container.firstChild).toMatchSnapshot()
+test('renders with a couple of uncategorized tracks', async () => {
+  const session = createTestSession()
+  session.addAssemblyConf({
+    name: 'volMyt1',
+    sequence: {
+      trackId: 'sequenceConfigId',
+      type: 'ReferenceSequenceTrack',
+      adapter: {
+        type: 'FromConfigSequenceAdapter',
+        features: [
+          {
+            refName: 'ctgA',
+            uniqueId: 'firstId',
+            start: 0,
+            end: 10,
+            seq: 'cattgttgcg',
+          },
+        ],
+      },
+    },
   })
-
-  it('renders with a couple of uncategorized tracks', async () => {
-    const session = createTestSession()
-    session.addAssemblyConf({
-      name: 'volMyt1',
-      sequence: {
-        trackId: 'sequenceConfigId',
-        type: 'ReferenceSequenceTrack',
-        adapter: {
-          type: 'FromConfigSequenceAdapter',
-          features: [
-            {
-              refName: 'ctgA',
-              uniqueId: 'firstId',
-              start: 0,
-              end: 10,
-              seq: 'cattgttgcg',
-            },
-          ],
-        },
+  session.addTrackConf({
+    trackId: 'fooC',
+    assemblyNames: ['volMyt1'],
+    type: 'FeatureTrack',
+    adapter: { type: 'FromConfigAdapter', features: [] },
+  })
+  session.addTrackConf({
+    trackId: 'barC',
+    assemblyNames: ['volMyt1'],
+    type: 'FeatureTrack',
+    adapter: { type: 'FromConfigAdapter', features: [] },
+  })
+  const firstView = session.addView('LinearGenomeView', {
+    displayedRegions: [
+      {
+        assemblyName: 'volMyt1',
+        refName: 'ctgA',
+        start: 0,
+        end: 1000,
       },
-    })
-    session.addTrackConf({
-      trackId: 'fooC',
-      assemblyNames: ['volMyt1'],
-      type: 'FeatureTrack',
-      adapter: { type: 'FromConfigAdapter', features: [] },
-    })
-    session.addTrackConf({
-      trackId: 'barC',
-      assemblyNames: ['volMyt1'],
-      type: 'FeatureTrack',
-      adapter: { type: 'FromConfigAdapter', features: [] },
-    })
-    const firstView = session.addView('LinearGenomeView', {
-      displayedRegions: [
-        {
-          assemblyName: 'volMyt1',
-          refName: 'ctgA',
-          start: 0,
-          end: 1000,
-        },
-      ],
-    })
-    firstView.showTrack(session.sessionTracks[0].trackId)
-    firstView.showTrack(session.sessionTracks[1].trackId)
-    const model = firstView.activateTrackSelector()
-
-    const { container, findByTestId } = render(
-      <ThemeProvider theme={createJBrowseTheme()}>
-        {/* @ts-ignore*/}
-        <HierarchicalTrackSelector model={model} />
-      </ThemeProvider>,
-    )
-    await findByTestId('hierarchical_track_selector')
-    expect(container.firstChild).toMatchSnapshot()
+    ],
   })
+  firstView.showTrack(session.sessionTracks[0].trackId)
+  firstView.showTrack(session.sessionTracks[1].trackId)
+  const model = firstView.activateTrackSelector()
 
-  it('renders with a couple of categorized tracks', async () => {
-    const session = createTestSession()
-    session.addAssemblyConf({
-      name: 'volMyt1',
-      sequence: {
-        trackId: 'sequenceConfigId',
-        type: 'ReferenceSequenceTrack',
-        adapter: {
-          type: 'FromConfigSequenceAdapter',
-          features: [
-            {
-              refName: 'ctgA',
-              uniqueId: 'firstId',
-              start: 0,
-              end: 10,
-              seq: 'cattgttgcg',
-            },
-          ],
-        },
-      },
-    })
+  const { container, findByTestId } = render(
+    <ThemeProvider theme={createJBrowseTheme()}>
+      {/* @ts-ignore*/}
+      <HierarchicalTrackSelector model={model} />
+    </ThemeProvider>,
+  )
+  await findByTestId('hierarchical_track_selector')
+  expect(container.firstChild).toMatchSnapshot()
+})
 
-    session.addTrackConf({
-      trackId: 'fooC',
-      assemblyNames: ['volMyt1'],
-      type: 'FeatureTrack',
-      adapter: { type: 'FromConfigAdapter', features: [] },
-    })
-    session.addTrackConf({
-      trackId: 'barC',
-      assemblyNames: ['volMyt1'],
-      type: 'FeatureTrack',
-      adapter: { type: 'FromConfigAdapter', features: [] },
-    })
-    const firstView = session.addView('LinearGenomeView', {
-      displayedRegions: [
-        {
-          assemblyName: 'volMyt1',
-          refName: 'ctgA',
-          start: 0,
-          end: 1000,
-        },
-      ],
-    })
-    firstView.showTrack(session.sessionTracks[0].trackId)
-    firstView.showTrack(session.sessionTracks[1].trackId)
-    firstView.tracks[0].configuration.category.set(['Foo Category'])
-    firstView.tracks[1].configuration.category.set([
-      'Foo Category',
-      'Bar Category',
-    ])
-    const model = firstView.activateTrackSelector()
+test('renders with a couple of categorized tracks', async () => {
+  const session = createTestSession()
+  session.addAssemblyConf({
+    name: 'volMyt1',
+    sequence: {
+      trackId: 'sequenceConfigId',
+      type: 'ReferenceSequenceTrack',
+      adapter: {
+        type: 'FromConfigSequenceAdapter',
+        features: [
+          {
+            refName: 'ctgA',
+            uniqueId: 'firstId',
+            start: 0,
+            end: 10,
+            seq: 'cattgttgcg',
+          },
+        ],
+      },
+    },
+  })
 
-    const { container, findByTestId } = render(
-      <ThemeProvider theme={createJBrowseTheme()}>
-        {/* @ts-ignore*/}
-        <HierarchicalTrackSelector model={model} />
-      </ThemeProvider>,
-    )
-    await findByTestId('hierarchical_track_selector')
-    expect(container.firstChild).toMatchSnapshot()
+  session.addTrackConf({
+    trackId: 'fooC',
+    assemblyNames: ['volMyt1'],
+    type: 'FeatureTrack',
+    adapter: { type: 'FromConfigAdapter', features: [] },
+  })
+  session.addTrackConf({
+    trackId: 'barC',
+    assemblyNames: ['volMyt1'],
+    type: 'FeatureTrack',
+    adapter: { type: 'FromConfigAdapter', features: [] },
   })
+  const firstView = session.addView('LinearGenomeView', {
+    displayedRegions: [
+      {
+        assemblyName: 'volMyt1',
+        refName: 'ctgA',
+        start: 0,
+        end: 1000,
+      },
+    ],
+  })
+  firstView.showTrack(session.sessionTracks[0].trackId)
+  firstView.showTrack(session.sessionTracks[1].trackId)
+  firstView.tracks[0].configuration.category.set(['Foo Category'])
+  firstView.tracks[1].configuration.category.set([
+    'Foo Category',
+    'Bar Category',
+  ])
+  const model = firstView.activateTrackSelector()
+
+  const { container, findByTestId } = render(
+    <ThemeProvider theme={createJBrowseTheme()}>
+      {/* @ts-ignore*/}
+      <HierarchicalTrackSelector model={model} />
+    </ThemeProvider>,
+  )
+  await findByTestId('hierarchical_track_selector')
+  expect(container.firstChild).toMatchSnapshot()
 })

package/src/HierarchicalTrackSelectorWidget/components/__snapshots__/HierarchicalTrackSelector.test.tsx.snap

@@ -1,6 +1,6 @@
 // Jest Snapshot v1, https://goo.gl/fbAQLP
 
-exports[`HierarchicalTrackSelector widget renders nothing with no assembly 1`] = `
+exports[`renders nothing with no assembly 1`] = `
 <button
   class="MuiButtonBase-root MuiFab-root MuiFab-circular MuiFab-sizeSmall MuiFab-secondary MuiFab-root MuiFab-circular MuiFab-sizeSmall MuiFab-secondary css-15opis6-MuiButtonBase-root-MuiFab-root-fab"
   tabindex="0"
@@ -23,7 +23,7 @@ exports[`HierarchicalTrackSelector widget renders nothing with no assembly 1`] =
 </button>
 `;
 
-exports[`HierarchicalTrackSelector widget renders with a couple of categorized tracks 1`] = `
+exports[`renders with a couple of categorized tracks 1`] = `
 <div
   data-testid="hierarchical_track_selector"
 >
@@ -81,7 +81,7 @@ exports[`HierarchicalTrackSelector widget renders with a couple of categorized t
         Filter tracks
       </label>
       <div
-        class="MuiInputBase-root MuiInput-root MuiInput-underline MuiInputBase-colorPrimary MuiInputBase-fullWidth MuiInputBase-formControl MuiInputBase-sizeSmall MuiInputBase-adornedEnd css-1wz39fi-MuiInputBase-root-MuiInput-root"
+        class="MuiInputBase-root MuiInput-root MuiInput-underline MuiInputBase-colorPrimary MuiInputBase-fullWidth MuiInputBase-formControl MuiInputBase-sizeSmall MuiInputBase-adornedEnd css-1blad95-MuiInputBase-root-MuiInput-root"
       >
         <input
           aria-invalid="false"
@@ -120,7 +120,7 @@ exports[`HierarchicalTrackSelector widget renders with a couple of categorized t
 </div>
 `;
 
-exports[`HierarchicalTrackSelector widget renders with a couple of uncategorized tracks 1`] = `
+exports[`renders with a couple of uncategorized tracks 1`] = `
 <div
   data-testid="hierarchical_track_selector"
 >
@@ -178,7 +178,7 @@ exports[`HierarchicalTrackSelector widget renders with a couple of uncategorized
         Filter tracks
       </label>
       <div
-        class="MuiInputBase-root MuiInput-root MuiInput-underline MuiInputBase-colorPrimary MuiInputBase-fullWidth MuiInputBase-formControl MuiInputBase-sizeSmall MuiInputBase-adornedEnd css-1wz39fi-MuiInputBase-root-MuiInput-root"
+        class="MuiInputBase-root MuiInput-root MuiInput-underline MuiInputBase-colorPrimary MuiInputBase-fullWidth MuiInputBase-formControl MuiInputBase-sizeSmall MuiInputBase-adornedEnd css-1blad95-MuiInputBase-root-MuiInput-root"
       >
         <input
           aria-invalid="false"

package/src/HierarchicalTrackSelectorWidget/index.ts

@@ -1,5 +1,22 @@
 import stateModelFactory, { HierarchicalTrackSelectorModel } from './model'
 import configSchema from './configSchema'
+import PluginManager from '@jbrowse/core/PluginManager'
+import { WidgetType } from '@jbrowse/core/pluggableElementTypes'
+import { lazy } from 'react'
 
 export { stateModelFactory, configSchema }
 export type { HierarchicalTrackSelectorModel }
+
+export default (pluginManager: PluginManager) => {
+  pluginManager.addWidgetType(() => {
+    return new WidgetType({
+      name: 'HierarchicalTrackSelectorWidget',
+      heading: 'Available tracks',
+      configSchema,
+      stateModel: stateModelFactory(pluginManager),
+      ReactComponent: lazy(
+        () => import('./components/HierarchicalTrackSelector'),
+      ),
+    })
+  })
+}