@jbrowse/plugin-data-management 2.6.1 → 2.6.2

package/src/AddTrackWidget/components/TextIndexingConfig.tsx

@@ -1,132 +0,0 @@
-import React, { useEffect, useState } from 'react'
-import {
-  Card,
-  CardContent,
-  IconButton,
-  InputLabel,
-  InputAdornment,
-  List,
-  ListItem,
-  Paper,
-  TextField,
-} from '@mui/material'
-import { makeStyles } from 'tss-react/mui'
-import { observer } from 'mobx-react'
-
-// icons
-import DeleteIcon from '@mui/icons-material/Delete'
-import AddIcon from '@mui/icons-material/Add'
-
-// locals
-import { AddTrackModel } from '../model'
-
-const useStyles = makeStyles()(theme => ({
-  paper: {
-    display: 'flex',
-    flexDirection: 'column',
-    padding: theme.spacing(1),
-  },
-
-  card: {
-    marginTop: theme.spacing(1),
-  },
-}))
-
-const TextIndexingConfig = observer(function ({
-  model,
-}: {
-  model: AddTrackModel
-}) {
-  const { classes } = useStyles()
-  const [value1, setValue1] = useState('')
-  const [value2, setValue2] = useState('')
-  const [attributes, setAttributes] = useState(['Name', 'ID'])
-  const [exclude, setExclude] = useState(['CDS', 'exon'])
-  const sections = [
-    {
-      label: 'Indexing attributes',
-      values: attributes,
-    },
-    {
-      label: 'Feature types to exclude',
-      values: exclude,
-    },
-  ]
-  useEffect(() => {
-    model.setTextIndexingConf({ attributes, exclude })
-  }, [model, attributes, exclude])
-
-  return (
-    <Paper className={classes.paper}>
-      <InputLabel>Indexing configuration</InputLabel>
-      {sections.map((section, index) => (
-        <Card raised key={section.label} className={classes.card}>
-          <CardContent>
-            <InputLabel>{section.label}</InputLabel>
-            <List disablePadding>
-              {section.values.map((val: string, idx: number) => (
-                <ListItem key={idx} disableGutters>
-                  <TextField
-                    value={val}
-                    InputProps={{
-                      endAdornment: (
-                        <InputAdornment position="end">
-                          <IconButton
-                            onClick={() => {
-                              const newAttr = section.values.filter(
-                                (_, i) => i !== idx,
-                              )
-                              index === 0
-                                ? setAttributes(newAttr)
-                                : setExclude(newAttr)
-                            }}
-                          >
-                            <DeleteIcon />
-                          </IconButton>
-                        </InputAdornment>
-                      ),
-                    }}
-                  />
-                </ListItem>
-              ))}
-              <ListItem disableGutters>
-                <TextField
-                  value={index === 0 ? value1 : value2}
-                  placeholder="add new"
-                  onChange={event => {
-                    index === 0
-                      ? setValue1(event.target.value)
-                      : setValue2(event.target.value)
-                  }}
-                  InputProps={{
-                    endAdornment: (
-                      <InputAdornment position="end">
-                        <IconButton
-                          onClick={() => {
-                            if (index === 0) {
-                              setAttributes([...attributes, value1])
-                              setValue1('')
-                            } else {
-                              setExclude([...exclude, value2])
-                              setValue2('')
-                            }
-                          }}
-                          disabled={index === 0 ? value1 === '' : value2 === ''}
-                          data-testid={`stringArrayAdd-Feat`}
-                        >
-                          <AddIcon />
-                        </IconButton>
-                      </InputAdornment>
-                    ),
-                  }}
-                />
-              </ListItem>
-            </List>
-          </CardContent>
-        </Card>
-      ))}
-    </Paper>
-  )
-})
-
-export default TextIndexingConfig

package/src/AddTrackWidget/components/TrackAdapterSelector.tsx

@@ -1,73 +0,0 @@
-import React from 'react'
-import { ListSubheader, MenuItem, TextField } from '@mui/material'
-import { makeStyles } from 'tss-react/mui'
-import { getEnv } from '@jbrowse/core/util'
-import { observer } from 'mobx-react'
-import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
-
-// locals
-import { AddTrackModel } from '../model'
-
-const useStyles = makeStyles()(theme => ({
-  spacing: {
-    marginBottom: theme.spacing(3),
-  },
-}))
-
-// collate adapters into a map with
-// key: category
-// value: array of adapters with that category
-function categorizeAdapters(adaptersList: AdapterType[]) {
-  const map = {} as { [key: string]: AdapterType[] }
-  adaptersList.forEach(adapter => {
-    const key = adapter.adapterMetadata?.category || 'Default'
-    if (!map[key]) {
-      map[key] = []
-    }
-    map[key].push(adapter)
-  })
-  return map
-}
-
-const TrackAdapterSelector = observer(({ model }: { model: AddTrackModel }) => {
-  const { classes } = useStyles()
-  const { trackAdapter } = model
-  const { pluginManager } = getEnv(model)
-  return (
-    <TextField
-      className={classes.spacing}
-      value={trackAdapter?.type !== 'UNKNOWN' ? trackAdapter?.type : ''}
-      label="Adapter type"
-      variant="outlined"
-      helperText="Select an adapter type"
-      select
-      fullWidth
-      onChange={event => model.setAdapterHint(event.target.value)}
-      SelectProps={{
-        // @ts-expect-error
-        SelectDisplayProps: { 'data-testid': 'adapterTypeSelect' },
-      }}
-    >
-      {Object.entries(
-        categorizeAdapters(
-          pluginManager
-            .getAdapterElements()
-            .filter(e => !e.adapterMetadata?.hiddenFromGUI),
-        ),
-      ).map(([key, val]) => {
-        // returning array avoids needing to use a react fragment which
-        // Select/TextField sub-elements disagree with
-        return [
-          <ListSubheader>{key}</ListSubheader>,
-          val.map(elt => (
-            <MenuItem key={elt.name} value={elt.name}>
-              {elt.displayName}
-            </MenuItem>
-          )),
-        ]
-      })}
-    </TextField>
-  )
-})
-
-export default TrackAdapterSelector

package/src/AddTrackWidget/components/TrackSourceSelect.tsx

@@ -1,48 +0,0 @@
-import React from 'react'
-import { FileSelector } from '@jbrowse/core/ui'
-import { AbstractRootModel } from '@jbrowse/core/util'
-import { Paper } from '@mui/material'
-import { makeStyles } from 'tss-react/mui'
-import { getRoot } from 'mobx-state-tree'
-import { observer } from 'mobx-react'
-
-// locals
-import { AddTrackModel } from '../model'
-
-const useStyles = makeStyles()(theme => ({
-  paper: {
-    padding: theme.spacing(2),
-  },
-  spacer: {
-    height: theme.spacing(8),
-  },
-}))
-
-function TrackSourceSelect({ model }: { model: AddTrackModel }) {
-  const { classes } = useStyles()
-  const rootModel = getRoot<AbstractRootModel>(model)
-
-  return (
-    <Paper className={classes.paper}>
-      <FileSelector
-        name="Main file"
-        description=""
-        location={model.trackData}
-        setLocation={model.setTrackData}
-        setName={model.setTrackName}
-        rootModel={rootModel}
-      />
-      <div className={classes.spacer} />
-      <FileSelector
-        name="Index file"
-        description="(Optional) The URL of the index file is automatically inferred from the URL of the main file if it is not supplied."
-        location={model.indexTrackData}
-        setLocation={model.setIndexTrackData}
-        setName={model.setTrackName}
-        rootModel={rootModel}
-      />
-    </Paper>
-  )
-}
-
-export default observer(TrackSourceSelect)

package/src/AddTrackWidget/components/TrackTypeSelector.tsx

@@ -1,46 +0,0 @@
-import React from 'react'
-import { MenuItem, TextField } from '@mui/material'
-import { getEnv } from '@jbrowse/core/util'
-import { observer } from 'mobx-react'
-import { makeStyles } from 'tss-react/mui'
-
-// locals
-import { AddTrackModel } from '../model'
-
-const useStyles = makeStyles()(theme => ({
-  spacing: {
-    marginBottom: theme.spacing(3),
-  },
-}))
-
-const TrackTypeSelector = observer(({ model }: { model: AddTrackModel }) => {
-  const { classes } = useStyles()
-  const { pluginManager } = getEnv(model)
-  const { trackType } = model
-  const trackTypes = pluginManager.getTrackElements()
-
-  return (
-    <TextField
-      className={classes.spacing}
-      value={trackType}
-      variant="outlined"
-      label="Track type"
-      helperText="Select track type"
-      select
-      fullWidth
-      onChange={event => model.setTrackType(event.target.value)}
-      SelectProps={{
-        // @ts-expect-error
-        SelectDisplayProps: { 'data-testid': 'trackTypeSelect' },
-      }}
-    >
-      {trackTypes.map(({ name, displayName }) => (
-        <MenuItem key={name} value={name}>
-          {displayName}
-        </MenuItem>
-      ))}
-    </TextField>
-  )
-})
-
-export default TrackTypeSelector

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')),
-    })
-  })
-}