@jbrowse/plugin-data-management 2.6.1 → 2.6.3

package/src/AddConnectionWidget/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 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/AddConnectionWidget/model.ts

@@ -1,7 +0,0 @@
-import { types } from 'mobx-state-tree'
-import { ElementId } from '@jbrowse/core/util/types/mst'
-
-export default types.model('AddConnectionModel', {
-  id: ElementId,
-  type: types.literal('AddConnectionWidget'),
-})

package/src/AddTrackWidget/components/AddTrackWidget.test.tsx

@@ -1,118 +0,0 @@
-import React from 'react'
-import { render, fireEvent } from '@testing-library/react'
-import { createTestSession } from '@jbrowse/web/src/rootModel'
-import AddTrackWidget from './AddTrackWidget'
-jest.mock('@jbrowse/web/src/makeWorkerInstance', () => () => {})
-
-function getSession() {
-  const session = createTestSession()
-  session.addAssemblyConf({
-    name: 'volMyt1',
-    sequence: {
-      trackId: 'ref0',
-      type: 'ReferenceSequenceTrack',
-      adapter: {
-        type: 'FromConfigSequenceAdapter',
-        features: [
-          {
-            refName: 'ctgA',
-            uniqueId: 'firstId',
-            start: 0,
-            end: 1000,
-            seq: 'cattgttgcggagttgaacaACGGCATTAGGAACACTTCCGTCTCtcacttttatacgattatgattggttctttagccttggtttagattggtagtagtagcggcgctaatgctacctgaattgagaactcgagcgggggctaggcaaattctgattcagcctgacttctcttggaaccctgcccataaatcaaagggttagtgcggccaaaacgttggacaacggtattagaagaccaacctgaccaccaaaccgtcaattaaccggtatcttctcggaaacggcggttctctcctagatagcgatctgtggtctcaccatgcaatttaaacaggtgagtaaagattgctacaaatacgagactagctgtcaccagatgctgttcatctgttggctccttggtcgctccgttgtacccaggctactttgaaagagcgcagaatacttagacggtatcgatcatggtagcatagcattctgataacatgtatggagttcgaacatccgtctggggccggacggtccgtttgaggttggttgatctgggtgatagtcagcaagatagacgttagataacaaattaaaggattttaccttagattgcgactagtacaacggtacatcggtgattcgcgctctactagatcacgctatgggtaccataaacaaacggtggaccttctcaagctggttgacgcctcagcaacataggcttcctcctccacgcatctcagcataaaaggcttataaactgcttctttgtgccagagcaactcaattaagcccttggtaccgtgggcacgcattctgtcacggtgaccaactgttcatcctgaatcgccgaatgggactatttggtacaggaatcaagcggatggcactactgcagcttatttacgacggtattcttaaagtttttaagacaatgtatttcatgggtagttcggtttgttttattgctacacaggctcttgtagacgacctacttagcactacgg',
-          },
-        ],
-      },
-    },
-  })
-  session.addTrackConf({
-    trackId: 'i3jUPmrgMOS',
-    type: 'FeatureTrack',
-    name: 'Filter Test',
-    assemblyNames: ['volMyt1'],
-    adapter: {
-      type: 'FromConfigAdapter',
-      features: [
-        {
-          uniqueId: 'one',
-          refName: 'ctgA',
-          start: 100,
-          end: 101,
-          type: 'foo',
-          name: 'Boris',
-          note: 'note for boris',
-        },
-        {
-          uniqueId: 'two',
-          refName: 'ctgA',
-          start: 110,
-          end: 111,
-          type: 'bar',
-          name: 'Theresa',
-          note: 'note for theresa',
-        },
-        {
-          uniqueId: 'three',
-          refName: 'ctgA',
-          start: 120,
-          end: 121,
-          type: 'baz',
-          name: 'Nigel',
-          note: 'note for nigel',
-        },
-        {
-          uniqueId: 'four',
-          refName: 'ctgA',
-          start: 130,
-          end: 131,
-          type: 'quux',
-          name: 'Geoffray',
-          note: 'note for geoffray',
-        },
-      ],
-    },
-    filterAttributes: ['type', 'start', 'end'],
-  })
-
-  const view = session.addView('LinearGenomeView', {
-    displayedRegions: [
-      {
-        assemblyName: 'volMyt1',
-        refName: 'ctgA',
-        start: 0,
-        end: 1000,
-      },
-    ],
-  })
-
-  const model = session.addWidget('AddTrackWidget', 'addTrackWidget', {
-    view: view.id,
-  })
-  return { session, model }
-}
-
-describe('<AddTrackWidget />', () => {
-  it('adds a track', async () => {
-    const { session, model } = getSession()
-    const { getByTestId, getAllByTestId, findByText, findAllByText } = render(
-      <AddTrackWidget model={model} />,
-    )
-    expect(session.sessionTracks.length).toBe(1)
-    fireEvent.change(getAllByTestId('urlInput')[0], {
-      target: { value: 'test.txt' },
-    })
-    fireEvent.click(getAllByTestId('addTrackNextButton')[0])
-    fireEvent.mouseDown(getByTestId('adapterTypeSelect'))
-    const bamAdapter = await findByText('BAM adapter')
-    fireEvent.click(bamAdapter)
-    fireEvent.change(getByTestId('trackNameInput'), {
-      target: { value: 'Test track name' },
-    })
-    fireEvent.mouseDown(getByTestId('trackTypeSelect'))
-    fireEvent.click(await findByText('Feature track'))
-    fireEvent.mouseDown(getByTestId('assemblyNameSelect'))
-    fireEvent.click((await findAllByText('volMyt1'))[1])
-    fireEvent.click(getAllByTestId('addTrackNextButton')[0])
-    expect(session.sessionTracks.length).toBe(2)
-  })
-})

package/src/AddTrackWidget/components/AddTrackWidget.tsx

@@ -1,43 +0,0 @@
-import React, { useState } from 'react'
-import { observer } from 'mobx-react'
-import { FormControl, FormHelperText, Select, MenuItem } from '@mui/material'
-import { getEnv } from '@jbrowse/core/util'
-
-// locals
-import { AddTrackModel } from '../model'
-import DefaultAddTrackWorkflow from './DefaultAddTrackWorkflow'
-import PasteConfigWorkflow from './PasteConfigWorkflow'
-
-function AddTrackSelector({ model }: { model: AddTrackModel }) {
-  const [val, setVal] = useState('Default add track workflow')
-  const { pluginManager } = getEnv(model)
-  const widgets = pluginManager.getAddTrackWorkflowElements()
-  const ComponentMap = {
-    'Default add track workflow': DefaultAddTrackWorkflow,
-    'Add track JSON': PasteConfigWorkflow,
-    ...Object.fromEntries(widgets.map(w => [w.name, w.ReactComponent])),
-  } as { [key: string]: React.FC<{ model: AddTrackModel }> }
-
-  // make sure the selected value is in the list
-  const val2 = ComponentMap[val] ? val : 'Default add track workflow'
-  const Component = ComponentMap[val2]
-  return (
-    <>
-      <FormControl>
-        <Select value={val2} onChange={event => setVal(event.target.value)}>
-          {Object.keys(ComponentMap).map(e => (
-            <MenuItem key={e} value={e}>
-              {e}
-            </MenuItem>
-          ))}
-        </Select>
-        <FormHelperText>Type of add track workflow</FormHelperText>
-      </FormControl>
-
-      <br />
-      <Component model={model} />
-    </>
-  )
-}
-
-export default observer(AddTrackSelector)

package/src/AddTrackWidget/components/ConfirmTrack.tsx

@@ -1,189 +0,0 @@
-import React, { useEffect, useState } from 'react'
-import {
-  Checkbox,
-  FormControl,
-  FormControlLabel,
-  Link,
-  TextField,
-  Typography,
-} from '@mui/material'
-import { makeStyles } from 'tss-react/mui'
-import {
-  supportedIndexingAdapters,
-  getSession,
-  isElectron,
-} from '@jbrowse/core/util'
-import { observer } from 'mobx-react'
-import { UNKNOWN } from '@jbrowse/core/util/tracks'
-import { AssemblySelector } from '@jbrowse/core/ui'
-
-// locals
-import { AddTrackModel } from '../model'
-import TextIndexingConfig from './TextIndexingConfig'
-import TrackTypeSelector from './TrackTypeSelector'
-import TrackAdapterSelector from './TrackAdapterSelector'
-
-const useStyles = makeStyles()(theme => ({
-  spacing: {
-    marginBottom: theme.spacing(3),
-  },
-}))
-
-function StatusMessage({
-  trackAdapter,
-  trackType,
-}: {
-  trackAdapter: { type: string; subadapter?: { type: string } }
-  trackType: string
-}) {
-  const { classes } = useStyles()
-  const { type, subadapter } = trackAdapter
-  return type === 'SNPCoverageAdapter' ? (
-    <Typography className={classes.spacing}>
-      Selected <code>{trackType}</code>. Using adapter <code>{type}</code> with
-      subadapter <code>{subadapter?.type}</code>. Please enter a track name and,
-      if necessary, update the track type.
-    </Typography>
-  ) : (
-    <Typography className={classes.spacing}>
-      Using adapter <code>{type}</code> and guessing track type{' '}
-      <code>{trackType}</code>. Please enter a track name and, if necessary,
-      update the track type.
-    </Typography>
-  )
-}
-
-function UnknownAdapterPrompt({ model }: { model: AddTrackModel }) {
-  const { classes } = useStyles()
-  return (
-    <>
-      <Typography className={classes.spacing}>
-        JBrowse was not able to guess the adapter type for this data, but it may
-        be in the list below. If not, you can{' '}
-        <Link
-          href="https://github.com/GMOD/jbrowse-components/releases"
-          target="_blank"
-          rel="noopener noreferrer"
-        >
-          check for new releases
-        </Link>{' '}
-        of JBrowse to see if they support this data type or{' '}
-        <Link
-          href="https://github.com/GMOD/jbrowse-components/issues/new"
-          target="_blank"
-          rel="noopener noreferrer"
-        >
-          file an issue
-        </Link>{' '}
-        and add a feature request for this data type.
-      </Typography>
-      <TrackAdapterSelector model={model} />
-    </>
-  )
-}
-
-export default observer(function ConfirmTrack({
-  model,
-}: {
-  model: AddTrackModel
-}) {
-  const { classes } = useStyles()
-  const [check, setCheck] = useState(true)
-  const session = getSession(model)
-  const { trackName, trackAdapter, trackType, warningMessage, adapterHint } =
-    model
-
-  useEffect(() => {
-    if (adapterHint === '' && trackAdapter) {
-      model.setAdapterHint(trackAdapter.type)
-    }
-  }, [adapterHint, trackAdapter, trackAdapter?.type, model])
-
-  if (model.unsupported) {
-    return (
-      <Typography className={classes.spacing}>
-        This version of JBrowse cannot display data of this type. It is
-        possible, however, that there is a newer version that can display them.
-        You can{' '}
-        <Link
-          href="https://github.com/GMOD/jbrowse-components/releases"
-          target="_blank"
-          rel="noopener noreferrer"
-        >
-          check for new releases
-        </Link>{' '}
-        of JBrowse or{' '}
-        <Link
-          href="https://github.com/GMOD/jbrowse-components/issues/new"
-          target="_blank"
-          rel="noopener noreferrer"
-        >
-          file an issue
-        </Link>{' '}
-        and add a feature request for this data type.
-      </Typography>
-    )
-  }
-  if (trackAdapter?.type === UNKNOWN) {
-    return <UnknownAdapterPrompt model={model} />
-  }
-
-  if (!trackAdapter?.type) {
-    return <Typography>Could not recognize this data type.</Typography>
-  }
-
-  const supportedForIndexing = supportedIndexingAdapters(trackAdapter?.type)
-  return (
-    <div>
-      {trackAdapter ? (
-        <StatusMessage trackAdapter={trackAdapter} trackType={trackType} />
-      ) : null}
-      {warningMessage ? (
-        <Typography style={{ color: 'orange' }}>{warningMessage}</Typography>
-      ) : null}
-      <TextField
-        className={classes.spacing}
-        label="trackName"
-        helperText="A name for this track"
-        fullWidth
-        value={trackName}
-        onChange={event => model.setTrackName(event.target.value)}
-        inputProps={{ 'data-testid': 'trackNameInput' }}
-      />
-      <TrackAdapterSelector model={model} />
-      <TrackTypeSelector model={model} />
-      <AssemblySelector
-        session={session}
-        helperText="Select assembly to add track to"
-        selected={model.assembly}
-        onChange={asm => model.setAssembly(asm)}
-        TextFieldProps={{
-          fullWidth: true,
-          SelectProps: {
-            // @ts-expect-error
-            SelectDisplayProps: { 'data-testid': 'assemblyNameSelect' },
-          },
-        }}
-      />
-      {isElectron && supportedForIndexing && (
-        <FormControl>
-          <FormControlLabel
-            label={'Index track for text searching?'}
-            control={
-              <Checkbox
-                checked={check}
-                onChange={e => {
-                  setCheck(e.target.checked)
-                  model.setTextIndexTrack(e.target.checked)
-                }}
-              />
-            }
-          />
-        </FormControl>
-      )}
-      {isElectron && check && supportedForIndexing ? (
-        <TextIndexingConfig model={model} />
-      ) : null}
-    </div>
-  )
-})

package/src/AddTrackWidget/components/DefaultAddTrackWorkflow.tsx

@@ -1,201 +0,0 @@
-import React, { useState } from 'react'
-import {
-  Alert,
-  Button,
-  Step,
-  StepContent,
-  StepLabel,
-  Stepper,
-  Typography,
-} from '@mui/material'
-import { makeStyles } from 'tss-react/mui'
-import { getRoot } from 'mobx-state-tree'
-
-import {
-  getSession,
-  isElectron,
-  supportedIndexingAdapters,
-} from '@jbrowse/core/util'
-import { getConf } from '@jbrowse/core/configuration'
-import { observer } from 'mobx-react'
-
-// locals
-import ConfirmTrack from './ConfirmTrack'
-import TrackSourceSelect from './TrackSourceSelect'
-import { AddTrackModel } from '../model'
-
-const useStyles = makeStyles()(theme => ({
-  root: {
-    marginTop: theme.spacing(1),
-  },
-  stepper: {
-    backgroundColor: theme.palette.background.default,
-  },
-  button: {
-    marginRight: theme.spacing(1),
-  },
-  actionsContainer: {
-    marginTop: theme.spacing(10),
-    marginBottom: theme.spacing(2),
-  },
-  alertContainer: {
-    padding: `${theme.spacing(2)}px 0px ${theme.spacing(2)}px 0px`,
-  },
-}))
-
-const steps = ['Enter track data', 'Confirm track type']
-
-function AddTrackWorkflow({ model }: { model: AddTrackModel }) {
-  const [activeStep, setActiveStep] = useState(0)
-  const { classes } = useStyles()
-
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  const { jobsManager } = getRoot<any>(model)
-  const session = getSession(model)
-  const {
-    assembly,
-    trackAdapter,
-    trackData,
-    trackName,
-    trackType,
-    textIndexTrack,
-    textIndexingConf,
-  } = model
-  const [trackErrorMessage, setTrackErrorMessage] = useState<string>()
-
-  function getStepContent(step: number) {
-    switch (step) {
-      case 0:
-        return <TrackSourceSelect model={model} />
-      case 1:
-        return <ConfirmTrack model={model} />
-      default:
-        return <Typography>Unknown step</Typography>
-    }
-  }
-
-  async function handleNext() {
-    if (activeStep !== steps.length - 1) {
-      setActiveStep(activeStep + 1)
-      return
-    }
-
-    const trackId = [
-      `${trackName.toLowerCase().replaceAll(' ', '_')}-${Date.now()}`,
-      `${session.adminMode ? '' : '-sessionTrack'}`,
-    ].join('')
-
-    const assemblyInstance = session.assemblyManager.get(assembly)
-
-    if (assemblyInstance && trackAdapter && trackAdapter.type !== 'UNKNOWN') {
-      session.addTrackConf({
-        trackId,
-        type: trackType,
-        name: trackName,
-        assemblyNames: [assembly],
-        adapter: {
-          ...trackAdapter,
-          sequenceAdapter: getConf(assemblyInstance, ['sequence', 'adapter']),
-        },
-      })
-      if (model.view) {
-        model.view.showTrack(trackId)
-        if (
-          isElectron &&
-          textIndexTrack &&
-          supportedIndexingAdapters(trackAdapter.type)
-        ) {
-          const attr = textIndexingConf || {
-            attributes: ['Name', 'ID'],
-            exclude: ['CDS', 'exon'],
-          }
-          const indexName = trackName + '-index'
-          const newEntry = {
-            indexingParams: {
-              ...attr,
-              assemblies: [assembly],
-              tracks: [trackId],
-              indexType: 'perTrack',
-              name: indexName,
-              timestamp: new Date().toISOString(),
-            },
-            name: indexName,
-            cancelCallback: () => jobsManager.abortJob(),
-          }
-          jobsManager.queueJob(newEntry)
-        }
-      } else {
-        session.notify(
-          'Open a new view, or use the track selector in an existing view, to view this track',
-          'info',
-        )
-      }
-      model.clearData()
-      session.hideWidget(model)
-    } else {
-      setTrackErrorMessage(
-        'Failed to add track.\nThe configuration of this file is not currently supported.',
-      )
-    }
-  }
-
-  function handleBack() {
-    setTrackErrorMessage(undefined)
-    setActiveStep(activeStep - 1)
-  }
-
-  function isNextDisabled() {
-    switch (activeStep) {
-      case 0:
-        return !trackData
-      case 1:
-        return !(trackName && trackType && trackAdapter?.type && assembly)
-      default:
-        return true
-    }
-  }
-
-  return (
-    <div className={classes.root}>
-      <Stepper
-        className={classes.stepper}
-        activeStep={activeStep}
-        orientation="vertical"
-      >
-        {steps.map((label, idx) => (
-          <Step key={label}>
-            <StepLabel>{label}</StepLabel>
-            <StepContent>
-              {getStepContent(idx)}
-              <div className={classes.actionsContainer}>
-                <Button
-                  disabled={activeStep === 0}
-                  onClick={handleBack}
-                  className={classes.button}
-                >
-                  Back
-                </Button>
-                <Button
-                  disabled={isNextDisabled()}
-                  variant="contained"
-                  color="primary"
-                  onClick={handleNext}
-                  className={classes.button}
-                  data-testid="addTrackNextButton"
-                >
-                  {activeStep === steps.length - 1 ? 'Add' : 'Next'}
-                </Button>
-              </div>
-              {trackErrorMessage ? (
-                <div className={classes.alertContainer}>
-                  <Alert severity="error">{trackErrorMessage}</Alert>
-                </div>
-              ) : null}
-            </StepContent>
-          </Step>
-        ))}
-      </Stepper>
-    </div>
-  )
-}
-export default observer(AddTrackWorkflow)

package/src/AddTrackWidget/components/PasteConfigWorkflow.tsx

@@ -1,65 +0,0 @@
-import React, { useState } from 'react'
-import { Button, TextField } from '@mui/material'
-import { ErrorMessage } from '@jbrowse/core/ui'
-import { makeStyles } from 'tss-react/mui'
-import { getSession } from '@jbrowse/core/util'
-import { observer } from 'mobx-react'
-
-// locals
-import { AddTrackModel } from '../model'
-
-const useStyles = makeStyles()({
-  textbox: {
-    width: '100%',
-  },
-  submit: {
-    marginTop: 25,
-    marginBottom: 100,
-    display: 'block',
-  },
-})
-
-function AddTrackWorkflow({ model }: { model: AddTrackModel }) {
-  const { classes } = useStyles()
-  const [val, setVal] = useState('')
-  const [error, setError] = useState<unknown>()
-
-  return (
-    <div>
-      {error ? <ErrorMessage error={error} /> : null}
-      <TextField
-        multiline
-        rows={10}
-        value={val}
-        onChange={event => setVal(event.target.value)}
-        placeholder={
-          'Paste track config or array of track configs in JSON format'
-        }
-        variant="outlined"
-        className={classes.textbox}
-      />
-      <Button
-        variant="contained"
-        className={classes.submit}
-        onClick={() => {
-          try {
-            setError(undefined)
-            const session = getSession(model)
-            const conf = JSON.parse(val)
-            const confs = Array.isArray(conf) ? conf : [conf]
-            confs.forEach(c => session.addTrackConf(c))
-            confs.forEach(c => c.trackId)
-            model.clearData()
-            session.hideWidget(model)
-          } catch (e) {
-            console.error(e)
-            setError(e)
-          }
-        }}
-      >
-        Submit
-      </Button>
-    </div>
-  )
-}
-export default observer(AddTrackWorkflow)