@jbrowse/plugin-data-management 2.5.0 → 2.6.2

package/src/AddTrackWidget/index.test.tsx

@@ -1,247 +0,0 @@
-import React from 'react'
-import { types } from 'mobx-state-tree'
-import PluginManager from '@jbrowse/core/PluginManager'
-import Plugin from '@jbrowse/core/Plugin'
-import ViewType from '@jbrowse/core/pluggableElementTypes/ViewType'
-import stateModelFactory from './model'
-import Alignments from '@jbrowse/plugin-alignments'
-import SVG from '@jbrowse/plugin-svg'
-import Variants from '@jbrowse/plugin-variants'
-import Hic from '@jbrowse/plugin-hic'
-
-function standardInitializer() {
-  const pluginManager = new PluginManager([
-    new FakeViewPlugin(),
-    new Alignments(),
-    new SVG(),
-    new Variants(),
-    new Hic(),
-  ])
-  pluginManager.createPluggableElements()
-  pluginManager.configure()
-
-  const SessionModel = types
-    .model({
-      view: FakeViewModel,
-      widget: stateModelFactory(pluginManager),
-    })
-    .volatile(() => ({
-      rpcManager: {},
-      configuration: {},
-    }))
-
-  // assemblyNames is defined on the view, which is done in LGV for example
-  // this is really just used for convenience to automatically fill in the
-  // assembly field in the form
-  return SessionModel.create(
-    {
-      view: {
-        id: 'testing',
-        type: 'FakeView',
-        assemblyNames: ['volvox'],
-      },
-      widget: {
-        type: 'AddTrackWidget',
-        view: 'testing',
-      },
-    },
-    { pluginManager },
-  )
-}
-
-const realLocation = window.location
-
-// https://stackoverflow.com/a/60110508/2129219
-function setWindowLoc(loc: string) {
-  // @ts-expect-error
-  delete window.location
-  // @ts-expect-error
-  window.location = new URL(loc)
-}
-
-const FakeViewModel = types.model('FakeView', {
-  id: types.identifier,
-  type: types.literal('FakeView'),
-  assemblyNames: types.maybe(types.array(types.string)),
-})
-
-// register a true fake view plugin because the widget.view is a true
-// safeReference to a pluginManager.pluggableMstType('view', 'stateModel')
-class FakeViewPlugin extends Plugin {
-  name = 'FakeViewPlugin'
-
-  install(pluginManager: PluginManager) {
-    pluginManager.addViewType(() => {
-      return new ViewType({
-        name: 'FakeView',
-        stateModel: FakeViewModel,
-        ReactComponent: () => <div>Hello world</div>,
-      })
-    })
-  }
-}
-
-describe('tests on an LGV type system with view.assemblyNames, using URL', () => {
-  let session: ReturnType<typeof standardInitializer>
-  beforeEach(() => {
-    session = standardInitializer()
-  })
-
-  afterEach(() => {
-    window.location = realLocation
-  })
-
-  it('adds relative URL (BAM)', () => {
-    const { widget } = session
-    widget.setTrackData({
-      uri: 'volvox-sorted.bam',
-      locationType: 'UriLocation',
-    })
-    expect(widget.trackName).toBe('volvox-sorted.bam')
-    expect(widget.isFtp).toBe(false)
-    expect(widget.isRelativeUrl).toBe(true)
-    expect(widget.assembly).toBe('volvox')
-    expect(widget.trackType).toBe('AlignmentsTrack')
-  })
-
-  it('adds full URL (BAM)', () => {
-    const { widget } = session
-    widget.setTrackData({
-      uri: 'http://google.com/volvox-sorted.bam',
-      locationType: 'UriLocation',
-    })
-    expect(widget.trackName).toBe('volvox-sorted.bam')
-    expect(widget.isRelativeUrl).toBe(false)
-    expect(widget.assembly).toBe('volvox')
-  })
-
-  it('test wrongProtocol returning false', () => {
-    const { widget } = session
-    widget.setTrackData({
-      uri: 'http://google.com/volvox-sorted.bam',
-      locationType: 'UriLocation',
-    })
-    setWindowLoc('http://google.com')
-
-    expect(widget.wrongProtocol).toBe(false)
-  })
-
-  it('test wrongProtocol returning true', () => {
-    const { widget } = session
-    widget.setTrackData({
-      uri: 'http://google.com/volvox-sorted.bam',
-      locationType: 'UriLocation',
-    })
-    setWindowLoc('https://google.com')
-    expect(widget.wrongProtocol).toBe(true)
-  })
-})
-
-test('tests on an view without view.assemblyNames', () => {
-  const pluginManager = new PluginManager([new FakeViewPlugin()])
-  pluginManager.createPluggableElements()
-  pluginManager.configure()
-
-  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',
-    },
-  })
-
-  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: ReturnType<typeof standardInitializer>
-  beforeEach(() => {
-    session = standardInitializer()
-  })
-
-  afterEach(() => {
-    window.location = realLocation
-  })
-
-  it('adds bam', () => {
-    const { widget } = session
-    widget.setTrackData({
-      uri: 'volvox-sorted.bam',
-      locationType: 'UriLocation',
-    })
-    expect(widget.trackType).toBe('AlignmentsTrack')
-  })
-
-  it('adds cram', () => {
-    const { widget } = session
-    widget.setTrackData({
-      uri: 'volvox-sorted.cram',
-      locationType: 'UriLocation',
-    })
-    expect(widget.trackType).toBe('AlignmentsTrack')
-  })
-
-  it('adds .vcf.gz', () => {
-    const { widget } = session
-    widget.setTrackData({
-      uri: 'volvox-sorted.vcf.gz',
-      locationType: 'UriLocation',
-    })
-    expect(widget.trackType).toBe('VariantTrack')
-  })
-
-  it('adds .gff3', () => {
-    const { widget } = session
-    widget.setTrackData({
-      uri: 'volvox-sorted.gff3',
-      locationType: 'UriLocation',
-    })
-    expect(widget.trackType).toBe('FeatureTrack')
-  })
-
-  it('adds .hic', () => {
-    const { widget } = session
-    widget.setTrackData({
-      uri: 'volvox-sorted.hic',
-      locationType: 'UriLocation',
-    })
-    expect(widget.trackType).toBe('HicTrack')
-  })
-})
-
-describe('tests localpath', () => {
-  let session: ReturnType<typeof standardInitializer>
-  beforeEach(() => {
-    session = standardInitializer()
-  })
-  it('adds bam', () => {
-    const { widget } = session
-    widget.setTrackData({
-      localPath: 'volvox-sorted.bam',
-      locationType: 'LocalPathLocation',
-    })
-    expect(widget.trackType).toBe('AlignmentsTrack')
-    expect(widget.trackName).toBe('volvox-sorted.bam')
-    // the localPath is not a "relativeUrl"
-    expect(widget.isRelativeUrl).toBe(false)
-    expect(widget.isFtp).toBe(false)
-    expect(widget.wrongProtocol).toBe(false)
-    expect(widget.assembly).toBe('volvox')
-  })
-})

package/src/AddTrackWidget/index.ts

@@ -1,19 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import { WidgetType } from '@jbrowse/core/pluggableElementTypes'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { lazy } from 'react'
-
-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/AddTrackWidget/model.ts

@@ -1,179 +0,0 @@
-import { types, Instance } from 'mobx-state-tree'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { ElementId } from '@jbrowse/core/util/types/mst'
-import { FileLocation } from '@jbrowse/core/util/types'
-import {
-  guessAdapter,
-  guessTrackType,
-  getFileName,
-  UNSUPPORTED,
-} from '@jbrowse/core/util/tracks'
-
-function isAbsoluteUrl(url = '') {
-  try {
-    new URL(url)
-    return true
-  } catch (error) {
-    return url.startsWith('/')
-  }
-}
-interface IndexingAttr {
-  attributes: string[]
-  exclude: string[]
-}
-export default function f(pluginManager: PluginManager) {
-  return types
-    .model('AddTrackModel', {
-      id: ElementId,
-      type: types.literal('AddTrackWidget'),
-      view: types.safeReference(
-        pluginManager.pluggableMstType('view', 'stateModel'),
-      ),
-    })
-    .volatile(() => ({
-      trackSource: 'fromFile',
-      trackData: undefined as FileLocation | undefined,
-      indexTrackData: undefined as FileLocation | undefined,
-
-      // alts
-      altAssemblyName: '',
-      altTrackName: '',
-      altTrackType: '',
-
-      adapterHint: '',
-      textIndexTrack: true,
-      textIndexingConf: undefined as IndexingAttr | undefined,
-    }))
-    .actions(self => ({
-      setAdapterHint(obj: string) {
-        self.adapterHint = obj
-      },
-      setTrackSource(str: string) {
-        self.trackSource = str
-      },
-      setTextIndexingConf(conf: IndexingAttr) {
-        self.textIndexingConf = conf
-      },
-      setTextIndexTrack(flag: boolean) {
-        self.textIndexTrack = flag
-      },
-      setTrackData(obj: FileLocation) {
-        self.trackData = obj
-      },
-      setIndexTrackData(obj: FileLocation) {
-        self.indexTrackData = obj
-      },
-      setAssembly(str: string) {
-        self.altAssemblyName = str
-      },
-      setTrackName(str: string) {
-        self.altTrackName = str
-      },
-      setTrackType(str: string) {
-        self.altTrackType = str
-      },
-
-      clearData() {
-        self.trackSource = ''
-        self.altTrackName = ''
-        self.altTrackType = ''
-        self.altAssemblyName = ''
-        self.adapterHint = ''
-        self.indexTrackData = undefined
-        self.trackData = undefined
-        self.textIndexingConf = undefined
-        self.textIndexTrack = true
-      },
-    }))
-    .views(self => ({
-      get trackAdapter() {
-        const { trackData, indexTrackData, adapterHint } = self
-
-        return trackData
-          ? guessAdapter(trackData, indexTrackData, adapterHint, self)
-          : undefined
-      },
-
-      get trackName() {
-        return (
-          self.altTrackName ||
-          (self.trackData ? getFileName(self.trackData) : '')
-        )
-      },
-
-      get isFtp() {
-        const { trackData: track, indexTrackData: index } = self
-        return !!(
-          // @ts-expect-error
-          (index?.uri?.startsWith('ftp://') || track?.uri?.startsWith('ftp://'))
-        )
-      },
-
-      get isRelativeTrackUrl() {
-        // @ts-expect-error
-        const uri = self.trackData?.uri
-        return uri ? !isAbsoluteUrl(uri) : false
-      },
-      get isRelativeIndexUrl() {
-        // @ts-expect-error
-        const uri = self.indexTrackData?.uri
-        return uri ? !isAbsoluteUrl(uri) : false
-      },
-      get isRelativeUrl() {
-        return this.isRelativeIndexUrl || this.isRelativeTrackUrl
-      },
-
-      get trackHttp() {
-        // @ts-expect-error
-        return self.trackData?.uri?.startsWith('http://')
-      },
-      get indexHttp() {
-        // @ts-expect-error
-        return self.indexTrackData?.uri?.startsWith('http://')
-      },
-
-      get wrongProtocol() {
-        return (
-          window.location.protocol === 'https:' &&
-          (this.trackHttp || this.indexHttp)
-        )
-      },
-
-      get unsupported() {
-        return this.trackAdapter?.type === UNSUPPORTED
-      },
-
-      get assembly() {
-        return self.altAssemblyName || self.view.assemblyNames?.[0]
-      },
-
-      get trackType() {
-        return (
-          self.altTrackType ||
-          (this.trackAdapter
-            ? guessTrackType(this.trackAdapter.type, self)
-            : '')
-        )
-      },
-    }))
-    .views(self => ({
-      get warningMessage() {
-        if (self.isFtp) {
-          return `Warning: JBrowse cannot access files using the ftp protocol`
-        } else if (self.isRelativeUrl) {
-          return `Warning: one or more of your files do not provide the protocol e.g.
-          https://, please provide an absolute URL unless you are sure a
-          relative URL is intended.`
-        } else if (self.wrongProtocol) {
-          return `Warning: You entered a http:// resources but we cannot access HTTP
-          resources from JBrowse when it is running on https. Please use an
-          https URL for your track, or access the JBrowse app from the http
-          protocol`
-        }
-        return ''
-      },
-    }))
-}
-
-export type AddTrackStateModel = ReturnType<typeof f>
-export type AddTrackModel = Instance<AddTrackStateModel>

package/src/AssemblyManager/AssemblyAddForm.tsx

@@ -1,250 +0,0 @@
-import React, { useState } from 'react'
-import { observer } from 'mobx-react'
-import { Button, Grid, MenuItem, Paper, TextField } from '@mui/material'
-import { FileSelector } from '@jbrowse/core/ui'
-import { FileLocation } from '@jbrowse/core/util/types'
-
-// icons
-import AddIcon from '@mui/icons-material/Add'
-
-const AdapterSelector = observer(function ({
-  adapterSelection,
-  setAdapterSelection,
-  adapterTypes,
-}: {
-  adapterSelection: string
-  setAdapterSelection: Function
-  adapterTypes: string[]
-}) {
-  return (
-    <TextField
-      value={adapterSelection}
-      label="Type"
-      select
-      helperText="Type of adapter to use"
-      fullWidth
-      onChange={event => setAdapterSelection(event.target.value)}
-    >
-      {adapterTypes.map(str => (
-        <MenuItem key={str} value={str}>
-          {str}
-        </MenuItem>
-      ))}
-    </TextField>
-  )
-})
-
-const AdapterInput = observer(
-  ({
-    adapterSelection,
-    fastaLocation,
-    setFastaLocation,
-    faiLocation,
-    setFaiLocation,
-    gziLocation,
-    setGziLocation,
-    twoBitLocation,
-    setTwoBitLocation,
-    chromSizesLocation,
-    setChromSizesLocation,
-  }: {
-    adapterSelection: string
-    fastaLocation: FileLocation
-    setFastaLocation: Function
-    faiLocation: FileLocation
-    setFaiLocation: Function
-    gziLocation: FileLocation
-    setGziLocation: Function
-    twoBitLocation: FileLocation
-    setTwoBitLocation: Function
-    chromSizesLocation: FileLocation
-    setChromSizesLocation: Function
-  }) => {
-    if (
-      adapterSelection === 'IndexedFastaAdapter' ||
-      adapterSelection === 'BgzipFastaAdapter'
-    ) {
-      return (
-        <Grid container spacing={2}>
-          <Grid item>
-            <FileSelector
-              name="fastaLocation"
-              location={fastaLocation}
-              setLocation={loc => setFastaLocation(loc)}
-            />
-          </Grid>
-          <Grid item>
-            <FileSelector
-              name="faiLocation"
-              location={faiLocation}
-              setLocation={loc => setFaiLocation(loc)}
-            />
-          </Grid>
-          {adapterSelection === 'BgzipFastaAdapter' ? (
-            <Grid item>
-              <FileSelector
-                name="gziLocation"
-                location={gziLocation}
-                setLocation={loc => setGziLocation(loc)}
-              />
-            </Grid>
-          ) : null}
-        </Grid>
-      )
-    }
-
-    if (adapterSelection === 'TwoBitAdapter') {
-      return (
-        <Grid container spacing={2}>
-          <Grid item>
-            <FileSelector
-              name="twoBitLocation"
-              location={twoBitLocation}
-              setLocation={loc => setTwoBitLocation(loc)}
-            />
-          </Grid>
-          <Grid item>
-            <FileSelector
-              name="chromSizesLocation (optional, can be added to speed up loading 2bit files with many contigs)"
-              location={chromSizesLocation}
-              setLocation={loc => setChromSizesLocation(loc)}
-            />
-          </Grid>
-        </Grid>
-      )
-    }
-
-    return null
-  },
-)
-
-const blank = { uri: '' } as FileLocation
-
-const AssemblyAddForm = observer(function ({
-  rootModel,
-  setFormOpen,
-}: {
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  rootModel: any
-  setFormOpen: Function
-}) {
-  const adapterTypes = [
-    'IndexedFastaAdapter',
-    'BgzipFastaAdapter',
-    'TwoBitAdapter',
-  ]
-
-  const [assemblyName, setAssemblyName] = useState('')
-  const [assemblyDisplayName, setAssemblyDisplayName] = useState('')
-  const [adapterSelection, setAdapterSelection] = useState(adapterTypes[0])
-  const [fastaLocation, setFastaLocation] = useState(blank)
-  const [faiLocation, setFaiLocation] = useState(blank)
-  const [gziLocation, setGziLocation] = useState(blank)
-  const [twoBitLocation, setTwoBitLocation] = useState(blank)
-  const [chromSizesLocation, setChromSizesLocation] = useState(blank)
-
-  function createAssembly() {
-    if (assemblyName === '') {
-      rootModel.session.notify("Can't create an assembly without a name")
-    } else {
-      setFormOpen(false)
-      let newAssembly
-      if (adapterSelection === 'IndexedFastaAdapter') {
-        newAssembly = {
-          name: assemblyName,
-          displayName: assemblyDisplayName,
-          sequence: {
-            adapter: {
-              type: 'IndexedFastaAdapter',
-              fastaLocation,
-              faiLocation,
-            },
-          },
-        }
-      } else if (adapterSelection === 'BgzipFastaAdapter') {
-        newAssembly = {
-          name: assemblyName,
-          displayName: assemblyDisplayName,
-          sequence: {
-            adapter: {
-              type: 'BgzipFastaAdapter',
-              fastaLocation,
-              faiLocation,
-              gziLocation,
-            },
-          },
-        }
-      } else if (adapterSelection === 'TwoBitAdapter') {
-        newAssembly = {
-          name: assemblyName,
-          displayName: assemblyDisplayName,
-          sequence: {
-            adapter: {
-              type: 'TwoBitAdapter',
-              twoBitLocation,
-              chromSizesLocation,
-            },
-          },
-        }
-      }
-      rootModel.jbrowse.addAssemblyConf(newAssembly)
-      rootModel.session.notify(
-        `Successfully added ${assemblyName} assembly to JBrowse 2`,
-        'success',
-      )
-    }
-  }
-
-  return (
-    <div>
-      <Paper>
-        <TextField
-          id="assembly-name"
-          inputProps={{ 'data-testid': 'assembly-name' }}
-          label="Assembly name"
-          helperText="The assembly name e.g. hg38"
-          variant="outlined"
-          value={assemblyName}
-          onChange={event => setAssemblyName(event.target.value)}
-        />
-        <TextField
-          id="assembly-name"
-          inputProps={{ 'data-testid': 'assembly-display-name' }}
-          label="Assembly display name"
-          helperText='A human readable display name for the assembly e.g. "Homo sapiens (hg38)"'
-          variant="outlined"
-          value={assemblyDisplayName}
-          onChange={event => setAssemblyDisplayName(event.target.value)}
-        />
-        <AdapterSelector
-          adapterSelection={adapterSelection}
-          setAdapterSelection={setAdapterSelection}
-          adapterTypes={adapterTypes}
-        />
-        <AdapterInput
-          adapterSelection={adapterSelection}
-          fastaLocation={fastaLocation}
-          setFastaLocation={setFastaLocation}
-          faiLocation={faiLocation}
-          setFaiLocation={setFaiLocation}
-          gziLocation={gziLocation}
-          setGziLocation={setGziLocation}
-          twoBitLocation={twoBitLocation}
-          setTwoBitLocation={setTwoBitLocation}
-          chromSizesLocation={chromSizesLocation}
-          setChromSizesLocation={setChromSizesLocation}
-        />
-      </Paper>
-      <Button
-        variant="contained"
-        color="secondary"
-        startIcon={<AddIcon />}
-        onClick={createAssembly}
-      >
-        Create new assembly
-      </Button>
-    </div>
-  )
-})
-
-export default AssemblyAddForm

package/src/AssemblyManager/AssemblyEditor.tsx

@@ -1,20 +0,0 @@
-import React from 'react'
-import { observer } from 'mobx-react'
-import { ConfigurationEditor } from '@jbrowse/plugin-config'
-
-const AssemblyEditor = observer(
-  ({
-    assembly,
-  }: {
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    assembly: any
-  }) => {
-    return (
-      <div style={{ maxHeight: 600, overflow: 'auto' }}>
-        <ConfigurationEditor model={{ target: assembly }} />
-      </div>
-    )
-  },
-)
-
-export default AssemblyEditor