@jbrowse/plugin-data-management 2.6.1 → 2.6.3

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

package/src/AssemblyManager/AssemblyManager.test.tsx

@@ -1,93 +0,0 @@
-import React from 'react'
-import { fireEvent, render } from '@testing-library/react'
-import AssemblyManager from './AssemblyManager'
-
-const mockRootModel = {
-  jbrowse: {
-    assemblies: [
-      {
-        name: 'testAssembly',
-        sequence: {
-          type: 'testSequenceTrack',
-          trackId: '',
-          adapter: {
-            type: 'testSeqAdapter',
-            twoBitLocation: {
-              uri: 'test.2bit',
-              locationType: 'UriLocation',
-            },
-          },
-        },
-      },
-    ],
-    addAssemblyConf: jest.fn(),
-    removeAssemblyConf: jest.fn(),
-  },
-  session: {
-    notify: jest.fn(),
-  },
-}
-
-describe('AssemblyManager GUI', () => {
-  it('renders successfully', () => {
-    const { getByText } = render(
-      <AssemblyManager rootModel={mockRootModel} onClose={() => {}} />,
-    )
-    expect(getByText('Assembly manager')).toBeTruthy()
-  })
-
-  it('opens up the Add Assembly Form when clicked', () => {
-    const { getByText } = render(
-      <AssemblyManager rootModel={mockRootModel} onClose={() => {}} />,
-    )
-    fireEvent.click(getByText('Add new assembly'))
-    expect(getByText('Create new assembly')).toBeTruthy()
-  })
-
-  it('calls addAssemblyConf from the Add Assembly form', () => {
-    const { getByText, getByTestId } = render(
-      <AssemblyManager rootModel={mockRootModel} onClose={() => {}} />,
-    )
-    fireEvent.click(getByText('Add new assembly'))
-
-    // enter a new assembly and submit
-    fireEvent.change(getByTestId('assembly-name'), {
-      target: {
-        value: 'ce11',
-      },
-    })
-    fireEvent.click(getByText('Create new assembly'))
-
-    expect(mockRootModel.jbrowse.addAssemblyConf).toHaveBeenCalledTimes(1)
-  })
-
-  it("prompts the user for a name when adding assembly if they don't", () => {
-    const { getByText } = render(
-      <AssemblyManager rootModel={mockRootModel} onClose={() => {}} />,
-    )
-    fireEvent.click(getByText('Add new assembly'))
-    fireEvent.click(getByText('Create new assembly'))
-    expect(mockRootModel.session.notify).toHaveBeenCalledWith(
-      "Can't create an assembly without a name",
-    )
-  })
-
-  it('deletes an assembly when delete button clicked', () => {
-    const { getByTestId } = render(
-      <AssemblyManager rootModel={mockRootModel} onClose={() => {}} />,
-    )
-    fireEvent.click(getByTestId('testAssembly-delete'))
-    expect(mockRootModel.jbrowse.removeAssemblyConf).toHaveBeenCalledWith(
-      'testAssembly',
-    )
-  })
-
-  it('closes when the Close button is clicked', () => {
-    const onClose = jest.fn()
-    const { getByText } = render(
-      <AssemblyManager rootModel={mockRootModel} onClose={onClose} />,
-    )
-    fireEvent.click(getByText('Close'))
-    expect(onClose).toHaveBeenCalled()
-  })
-})

package/src/AssemblyManager/AssemblyManager.tsx

@@ -1,84 +0,0 @@
-import React, { useState } from 'react'
-import { observer } from 'mobx-react'
-import { AnyConfigurationModel } from '@jbrowse/core/configuration'
-import { Button, DialogActions, DialogContent } from '@mui/material'
-import { Dialog } from '@jbrowse/core/ui'
-
-// icons
-import AddIcon from '@mui/icons-material/Add'
-
-// locals
-import AssemblyTable from './AssemblyTable'
-import AssemblyAddForm from './AssemblyAddForm'
-import AssemblyEditor from './AssemblyEditor'
-
-const AssemblyManager = observer(function ({
-  rootModel,
-  onClose,
-}: {
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  rootModel: any
-  onClose: (arg: boolean) => void
-}) {
-  const [isFormOpen, setFormOpen] = useState(false)
-  const [isAssemblyBeingEdited, setIsAssemblyBeingEdited] = useState(false)
-  const [assemblyBeingEdited, setAssemblyBeingEdited] =
-    useState<AnyConfigurationModel>()
-
-  const showAssemblyTable = !isFormOpen && !isAssemblyBeingEdited
-
-  return (
-    <Dialog open onClose={() => onClose(false)} title="Assembly manager">
-      <DialogContent>
-        {showAssemblyTable ? (
-          <AssemblyTable
-            rootModel={rootModel}
-            setIsAssemblyBeingEdited={setIsAssemblyBeingEdited}
-            setAssemblyBeingEdited={setAssemblyBeingEdited}
-          />
-        ) : null}
-        {isAssemblyBeingEdited ? (
-          <AssemblyEditor assembly={assemblyBeingEdited} />
-        ) : null}
-        {isFormOpen ? (
-          <AssemblyAddForm rootModel={rootModel} setFormOpen={setFormOpen} />
-        ) : null}
-      </DialogContent>
-      <DialogActions>
-        {isFormOpen ? (
-          <Button variant="contained" onClick={() => setFormOpen(false)}>
-            Back
-          </Button>
-        ) : null}
-        {isAssemblyBeingEdited ? (
-          <Button
-            variant="contained"
-            onClick={() => setIsAssemblyBeingEdited(false)}
-          >
-            Back
-          </Button>
-        ) : null}
-        {showAssemblyTable ? (
-          <>
-            <Button
-              color="secondary"
-              variant="contained"
-              onClick={() => onClose(false)}
-            >
-              Close
-            </Button>
-            <Button
-              variant="contained"
-              startIcon={<AddIcon />}
-              onClick={() => setFormOpen(true)}
-            >
-              Add new assembly
-            </Button>
-          </>
-        ) : null}
-      </DialogActions>
-    </Dialog>
-  )
-})
-
-export default AssemblyManager