@jbrowse/plugin-data-management 2.3.1 → 2.3.3

package/src/ucsc-trackhub/ucscTrackHub.ts

@@ -0,0 +1,326 @@
+/* eslint-disable @typescript-eslint/no-explicit-any */
+import { RaStanza, TrackDbFile } from '@gmod/ucsc-hub'
+import { FileLocation, isUriLocation, objectHash } from '@jbrowse/core/util'
+import { openLocation } from '@jbrowse/core/util/io'
+import {
+  generateUnsupportedTrackConf,
+  generateUnknownTrackConf,
+} from '@jbrowse/core/util/tracks'
+import ucscAssemblies from './ucscAssemblies'
+
+export { ucscAssemblies }
+
+export async function fetchHubFile(hubLocation: FileLocation) {
+  try {
+    const hubFileText = await openLocation(hubLocation).readFile('utf8')
+    const { HubFile } = await import('@gmod/ucsc-hub')
+    return new HubFile(hubFileText)
+  } catch (error) {
+    throw new Error(`Not a valid hub.txt file, got error: '${error}'`)
+  }
+}
+
+export async function fetchGenomesFile(genomesLoc: FileLocation) {
+  const genomesFileText = await openLocation(genomesLoc).readFile('utf8')
+  const { GenomesFile } = await import('@gmod/ucsc-hub')
+  return new GenomesFile(genomesFileText)
+}
+
+export async function fetchTrackDbFile(trackDbLoc: FileLocation) {
+  const text = await openLocation(trackDbLoc).readFile('utf8')
+  const { TrackDbFile } = await import('@gmod/ucsc-hub')
+  return new TrackDbFile(text)
+}
+
+export function makeLoc(first: string, base: { uri: string }) {
+  return {
+    uri: new URL(first, base.uri).href,
+    locationType: 'UriLocation',
+  }
+}
+
+export function makeLocAlt(first: string, alt: string, base: { uri: string }) {
+  return first ? makeLoc(first, base) : makeLoc(alt, base)
+}
+
+export function makeLoc2(first: string, alt?: string) {
+  return first
+    ? {
+        uri: first,
+        locationType: 'LocalPath',
+      }
+    : {
+        uri: alt,
+        locationType: 'UriLocation',
+      }
+}
+
+export function generateTracks(
+  trackDb: TrackDbFile,
+  trackDbLoc: FileLocation,
+  assemblyName: string,
+  sequenceAdapter: any,
+) {
+  const tracks: any = []
+
+  trackDb.forEach((track, trackName) => {
+    const trackKeys = Array.from(track.keys()) as string[]
+    const parentTrackKeys = [
+      'superTrack',
+      'compositeTrack',
+      'container',
+      'view',
+    ]
+    if (trackKeys.some(key => parentTrackKeys.includes(key))) {
+      return
+    }
+    const parentTracks = []
+    let currentTrackName = trackName
+    do {
+      currentTrackName = trackDb.get(currentTrackName)?.get('parent') || ''
+      if (currentTrackName) {
+        ;[currentTrackName] = currentTrackName.split(' ')
+        parentTracks.push(trackDb.get(currentTrackName))
+      }
+    } while (currentTrackName)
+    parentTracks.reverse()
+    const categories = parentTracks
+      .map(p => p?.get('shortLabel'))
+      .filter((f): f is string => !!f)
+    const res = makeTrackConfig(
+      track,
+      categories,
+      trackDbLoc,
+      trackDb,
+      sequenceAdapter,
+    )
+    tracks.push({
+      ...res,
+      trackId: `ucsc-trackhub-${objectHash(res)}`,
+      assemblyNames: [assemblyName],
+    })
+  })
+
+  return tracks
+}
+
+function makeTrackConfig(
+  track: RaStanza,
+  categories: string[],
+  trackDbLoc: FileLocation,
+  trackDb: TrackDbFile,
+  sequenceAdapter: any,
+) {
+  let trackType = track.get('type')
+  const name = track.get('shortLabel') || ''
+  const bigDataUrl = track.get('bigDataUrl') || ''
+  const bigDataIdx = track.get('bigDataIndex') || ''
+  const isUri = isUriLocation(trackDbLoc)
+  if (!trackType) {
+    trackType = trackDb.get(track.get('parent') || '')?.get('type')
+  }
+  let baseTrackType = trackType?.split(' ')[0] || ''
+  if (baseTrackType === 'bam' && bigDataUrl.toLowerCase().endsWith('cram')) {
+    baseTrackType = 'cram'
+  }
+  const bigDataLocation = isUri
+    ? makeLoc(bigDataUrl, trackDbLoc)
+    : makeLoc2(bigDataUrl)
+
+  switch (baseTrackType) {
+    case 'bam':
+      return {
+        type: 'AlignmentsTrack',
+        name: track.get('shortLabel'),
+        description: track.get('longLabel'),
+        category: categories,
+        adapter: {
+          type: 'BamAdapter',
+          bamLocation: bigDataLocation,
+          index: {
+            location: isUri
+              ? makeLocAlt(bigDataIdx, bigDataUrl + '.bai', trackDbLoc)
+              : makeLoc2(bigDataIdx, bigDataUrl + '.bai'),
+          },
+        },
+      }
+
+    case 'bigBarChart':
+      return {
+        type: 'FeatureTrack',
+        name,
+        description: track.get('longLabel'),
+        category: categories,
+        adapter: {
+          type: 'BigBedAdapter',
+          bigBedLocation: bigDataLocation,
+        },
+        renderer: {
+          type: 'SvgFeatureRenderer',
+        },
+      }
+    case 'bigBed':
+      return {
+        type: 'FeatureTrack',
+        name,
+        description: track.get('longLabel'),
+        category: categories,
+        adapter: {
+          type: 'BigBedAdapter',
+          bigBedLocation: bigDataLocation,
+        },
+      }
+    case 'bigGenePred':
+      return {
+        type: 'FeatureTrack',
+        name,
+        description: track.get('longLabel'),
+        category: categories,
+        adapter: {
+          type: 'BigBedAdapter',
+          bigBedLocation: bigDataLocation,
+        },
+      }
+    case 'bigChain':
+      return {
+        type: 'FeatureTrack',
+        name,
+        description: track.get('longLabel'),
+        category: categories,
+        adapter: {
+          type: 'BigBedAdapter',
+          bigBedLocation: bigDataLocation,
+        },
+        renderer: {
+          type: 'SvgFeatureRenderer',
+        },
+      }
+    case 'bigInteract':
+      return {
+        type: 'FeatureTrack',
+        name,
+        description: track.get('longLabel'),
+        category: categories,
+        adapter: {
+          type: 'BigBedAdapter',
+          bigBedLocation: bigDataLocation,
+        },
+        renderer: {
+          type: 'SvgFeatureRenderer',
+        },
+      }
+    case 'bigMaf':
+      return {
+        type: 'FeatureTrack',
+        name,
+        description: track.get('longLabel'),
+        category: categories,
+        adapter: {
+          type: 'BigBedAdapter',
+          bigBedLocation: bigDataLocation,
+        },
+        renderer: {
+          type: 'SvgFeatureRenderer',
+        },
+      }
+    case 'bigPsl':
+      return {
+        type: 'FeatureTrack',
+        name,
+        description: track.get('longLabel'),
+        category: categories,
+        adapter: {
+          type: 'BigBedAdapter',
+          bigBedLocation: bigDataLocation,
+        },
+        renderer: {
+          type: 'SvgFeatureRenderer',
+        },
+      }
+    case 'bigWig':
+      return {
+        type: 'QuantitativeTrack',
+        name,
+        description: track.get('longLabel'),
+        category: categories,
+        adapter: {
+          type: 'BigWigAdapter',
+          bigWigLocation: bigDataLocation,
+        },
+      }
+
+    case 'cram':
+      return {
+        type: 'AlignmentsTrack',
+        name,
+        description: track.get('longLabel'),
+        category: categories,
+        adapter: {
+          type: 'CramAdapter',
+          cramLocation: bigDataLocation,
+          craiLocation: isUri
+            ? makeLocAlt(bigDataIdx, bigDataUrl + '.crai', trackDbLoc)
+            : makeLoc2(bigDataIdx, bigDataUrl + '.crai'),
+          sequenceAdapter,
+        },
+      }
+
+    case 'bigNarrowPeak':
+      return {
+        type: 'FeatureTrack',
+        name,
+        description: track.get('longLabel'),
+        category: categories,
+        adapter: {
+          type: 'BigBedAdapter',
+          bigBedLocation: bigDataLocation,
+        },
+      }
+    case 'peptideMapping':
+      return generateUnsupportedTrackConf(name, baseTrackType, categories)
+    case 'vcfTabix':
+      return {
+        type: 'VariantTrack',
+        name,
+        description: track.get('longLabel'),
+        category: categories,
+        adapter: {
+          type: 'VcfTabixAdapter',
+          vcfGzLocation: bigDataLocation,
+          index: {
+            location: isUri
+              ? makeLocAlt(bigDataIdx, bigDataUrl + '.tbi', trackDbLoc)
+              : makeLoc2(bigDataIdx, bigDataUrl + '.tbi'),
+          },
+        },
+      }
+
+    case 'hic':
+      return {
+        type: 'HicTrack',
+        name,
+        description: track.get('longLabel'),
+        category: categories,
+        adapter: {
+          type: 'HicAdapter',
+          hicLocation: bigDataLocation,
+        },
+      }
+
+    // unsupported types
+    //     case 'gvf':
+    //     case 'ld2':
+    //     case 'narrowPeak':
+    //     case 'wig':
+    //     case 'wigMaf':
+    //     case 'halSnake':
+    //     case 'bed':
+    //     case 'bed5FloatScore':
+    //     case 'bedGraph':
+    //     case 'bedRnaElements':
+    //     case 'broadPeak':
+    //     case 'coloredExon':
+    default:
+      return generateUnknownTrackConf(name, baseTrackType, categories)
+  }
+}

package/src/PluginStoreWidget/components/PluginStoreWidget.test.js

@@ -1,123 +0,0 @@
-import React from 'react'
-import { getSnapshot, getParent } from 'mobx-state-tree'
-import { ThemeProvider } from '@mui/material/styles'
-import { render, cleanup, fireEvent, waitFor } from '@testing-library/react'
-import { createJBrowseTheme } from '@jbrowse/core/ui'
-import { createTestSession } from '@jbrowse/web/src/rootModel'
-
-import PluginStoreWidget from './PluginStoreWidget'
-jest.mock('@jbrowse/web/src/makeWorkerInstance', () => () => {})
-
-const plugins = {
-  plugins: [
-    {
-      name: 'MsaView',
-      authors: ['Colin Diesh'],
-      description: 'multiple sequence alignment browser plugin for JBrowse 2',
-      location: 'https://github.com/GMOD/jbrowse-plugin-msaview',
-      url: 'https://unpkg.com/jbrowse-plugin-msaview/dist/jbrowse-plugin-msaview.umd.production.min.js',
-      license: 'Apache License 2.0',
-      image:
-        'https://raw.githubusercontent.com/GMOD/jbrowse-plugin-list/main/img/msaview-screenshot-fs8.png',
-    },
-  ],
-}
-
-describe('<PluginStoreWidget />', () => {
-  let session
-  let model
-
-  beforeEach(() => {
-    session = createTestSession()
-    model = session.addWidget('PluginStoreWidget', 'pluginStoreWidget')
-    const { location } = window
-    delete window.location
-    window.location = {
-      ...location,
-      reload: jest.fn(),
-    }
-    fetch.resetMocks()
-    fetch.mockResponse(JSON.stringify(plugins))
-  })
-
-  afterEach(cleanup)
-
-  it('renders with the available plugins', async () => {
-    const { container, findByText } = render(
-      <ThemeProvider theme={createJBrowseTheme()}>
-        <PluginStoreWidget model={model} />
-      </ThemeProvider>,
-    )
-    await findByText('multiple sequence alignment browser plugin for JBrowse 2')
-    expect(container.firstChild).toMatchSnapshot()
-  })
-
-  it('Installs a session plugin', async () => {
-    const { findByText } = render(
-      <ThemeProvider theme={createJBrowseTheme()}>
-        <PluginStoreWidget model={model} />
-      </ThemeProvider>,
-    )
-    await findByText('multiple sequence alignment browser plugin for JBrowse 2')
-    fireEvent.click(await findByText('Install'))
-    await waitFor(() => {
-      expect(window.location.reload).toHaveBeenCalled()
-    })
-    expect(getSnapshot(session.sessionPlugins)[0]).toEqual(plugins.plugins[0])
-  })
-
-  it('plugin store admin - adds a custom plugin correctly', async () => {
-    session = createTestSession({}, true)
-    model = session.addWidget('PluginStoreWidget', 'pluginStoreWidget')
-    const { findByText, getByText, getByLabelText } = render(
-      <ThemeProvider theme={createJBrowseTheme()}>
-        <PluginStoreWidget model={model} />
-      </ThemeProvider>,
-    )
-    await findByText('multiple sequence alignment browser plugin for JBrowse 2')
-    fireEvent.click(getByText('Add custom plugin'))
-    fireEvent.change(getByLabelText('Plugin URL'), {
-      target: {
-        value:
-          'https://unpkg.com/jbrowse-plugin-msaview/dist/jbrowse-plugin-msaview.esm.js',
-      },
-    })
-    fireEvent.change(getByLabelText('Plugin name'), {
-      target: {
-        value: 'MsaView',
-      },
-    })
-    fireEvent.click(getByText('Submit'))
-
-    await waitFor(() => {
-      expect(window.location.reload).toHaveBeenCalled()
-    })
-
-    expect(getSnapshot(getParent(session)).jbrowse.plugins).toEqual([
-      {
-        name: 'MsaView',
-        umdUrl:
-          'https://unpkg.com/jbrowse-plugin-msaview/dist/jbrowse-plugin-msaview.esm.js',
-      },
-    ])
-  })
-
-  it('plugin store admin - removes a custom plugin correctly', async () => {
-    session = createTestSession({}, true)
-    model = session.addWidget('PluginStoreWidget', 'pluginStoreWidget')
-    const rootModel = getParent(session)
-    const { jbrowse } = rootModel
-    jbrowse.addPlugin(plugins.plugins[0])
-    const { findByText, getByText, getByTestId } = render(
-      <ThemeProvider theme={createJBrowseTheme()}>
-        <PluginStoreWidget model={model} />
-      </ThemeProvider>,
-    )
-    await findByText('multiple sequence alignment browser plugin for JBrowse 2')
-    fireEvent.click(getByTestId('removePlugin-SVGPlugin'))
-    fireEvent.click(getByText('Confirm'))
-    await waitFor(() => {
-      expect(window.location.reload).toHaveBeenCalled()
-    })
-  })
-})

package/src/__snapshots__/index.test.js.snap

@@ -1,9 +0,0 @@
-// Jest Snapshot v1, https://goo.gl/fbAQLP
-
-exports[`Data management adds config editor widget 1`] = `{}`;
-
-exports[`Data management adds connection add widget 1`] = `{}`;
-
-exports[`Data management adds hierarchical track selector 1`] = `{}`;
-
-exports[`Data management adds track add widget 1`] = `{}`;

package/src/index.test.js

@@ -1,61 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import Config from '@jbrowse/plugin-config'
-import { getSnapshot } from 'mobx-state-tree'
-import ThisPlugin from '.'
-
-describe('Data management', () => {
-  let pluginManager
-
-  beforeAll(() => {
-    const originalConsoleWarn = console.warn
-    console.warn = jest.fn()
-    pluginManager = new PluginManager([new ThisPlugin(), new Config()])
-    pluginManager.createPluggableElements()
-    pluginManager.configure()
-    console.warn = originalConsoleWarn
-  })
-
-  it("won't add if already added", () => {
-    expect(() => pluginManager.addPlugin(new ThisPlugin())).toThrow(
-      /JBrowse already configured, cannot add plugins/,
-    )
-  })
-
-  it('adds track add widget', () => {
-    const AddTrackWidget = pluginManager.getWidgetType('AddTrackWidget')
-    const config = AddTrackWidget.configSchema.create({
-      type: 'AddTrackWidget',
-    })
-    expect(getSnapshot(config)).toMatchSnapshot()
-  })
-
-  it('adds config editor widget', () => {
-    const ConfigurationEditorWidget = pluginManager.getWidgetType(
-      'ConfigurationEditorWidget',
-    )
-    const config = ConfigurationEditorWidget.configSchema.create({
-      type: 'ConfigurationEditorWidget',
-    })
-    expect(getSnapshot(config)).toMatchSnapshot()
-  })
-
-  it('adds connection add widget', () => {
-    const AddConnectionWidget = pluginManager.getWidgetType(
-      'AddConnectionWidget',
-    )
-    const config = AddConnectionWidget.configSchema.create({
-      type: 'AddConnectionWidget',
-    })
-    expect(getSnapshot(config)).toMatchSnapshot()
-  })
-
-  it('adds hierarchical track selector', () => {
-    const HierarchicalTrackSelectorWidget = pluginManager.getWidgetType(
-      'HierarchicalTrackSelectorWidget',
-    )
-    const config = HierarchicalTrackSelectorWidget.configSchema.create({
-      type: 'HierarchicalTrackSelectorWidget',
-    })
-    expect(getSnapshot(config)).toMatchSnapshot()
-  })
-})