@jbrowse/plugin-data-management 2.5.0 → 2.6.2

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

package/src/AssemblyManager/AssemblyTable.tsx

@@ -1,88 +0,0 @@
-import React from 'react'
-import { observer } from 'mobx-react'
-import {
-  IconButton,
-  Table,
-  TableBody,
-  TableCell,
-  TableContainer,
-  TableHead,
-  TableRow,
-  Paper,
-} from '@mui/material'
-import {
-  readConfObject,
-  AnyConfigurationModel,
-} from '@jbrowse/core/configuration'
-
-import CreateIcon from '@mui/icons-material/Create'
-import DeleteIcon from '@mui/icons-material/Delete'
-
-const AssemblyTable = observer(function ({
-  rootModel,
-  setIsAssemblyBeingEdited,
-  setAssemblyBeingEdited,
-}: {
-  rootModel: {
-    jbrowse: {
-      removeAssemblyConf: (arg: string) => void
-      assemblies: AnyConfigurationModel[]
-    }
-  }
-  setIsAssemblyBeingEdited(arg: boolean): void
-  setAssemblyBeingEdited(arg: AnyConfigurationModel): void
-}) {
-  function removeAssembly(name: string) {
-    rootModel.jbrowse.removeAssemblyConf(name)
-  }
-
-  const { assemblies } = rootModel.jbrowse
-
-  return (
-    <TableContainer component={Paper}>
-      <Table>
-        <TableHead>
-          <TableRow>
-            <TableCell>Name</TableCell>
-            <TableCell>Display name</TableCell>
-            <TableCell>Aliases</TableCell>
-            <TableCell>Actions</TableCell>
-          </TableRow>
-        </TableHead>
-        <TableBody>
-          {assemblies.map(assembly => {
-            const name = readConfObject(assembly, 'name')
-            const displayName = readConfObject(assembly, 'displayName')
-            const aliases = readConfObject(assembly, 'aliases')
-            return (
-              <TableRow key={name}>
-                <TableCell>{name}</TableCell>
-                <TableCell>{displayName}</TableCell>
-                <TableCell>{aliases ? aliases.toString() : ''}</TableCell>
-                <TableCell>
-                  <IconButton
-                    data-testid={`${name}-edit`}
-                    onClick={() => {
-                      setIsAssemblyBeingEdited(true)
-                      setAssemblyBeingEdited(assembly)
-                    }}
-                  >
-                    <CreateIcon color="primary" />
-                  </IconButton>
-                  <IconButton
-                    data-testid={`${name}-delete`}
-                    onClick={() => removeAssembly(name)}
-                  >
-                    <DeleteIcon color="error" />
-                  </IconButton>
-                </TableCell>
-              </TableRow>
-            )
-          })}
-        </TableBody>
-      </Table>
-    </TableContainer>
-  )
-})
-
-export default AssemblyTable

package/src/AssemblyManager/index.ts

@@ -1 +0,0 @@
-export { default } from './AssemblyManager'

package/src/HierarchicalTrackSelectorWidget/components/HierarchicalFab.tsx

@@ -1,94 +0,0 @@
-import React, { useState } from 'react'
-import { Fab, Menu, MenuItem } from '@mui/material'
-import { makeStyles } from 'tss-react/mui'
-import {
-  getSession,
-  isSessionModelWithWidgets,
-  isSessionModelWithConnections,
-  isSessionWithAddTracks,
-} from '@jbrowse/core/util'
-import { observer } from 'mobx-react'
-
-// icons
-import AddIcon from '@mui/icons-material/Add'
-
-// locals
-import { HierarchicalTrackSelectorModel } from '../model'
-
-const useStyles = makeStyles()(theme => ({
-  fab: {
-    position: 'absolute',
-    bottom: theme.spacing(6),
-    right: theme.spacing(6),
-  },
-}))
-
-export default observer(function HierarchicalFab({
-  model,
-}: {
-  model: HierarchicalTrackSelectorModel
-}) {
-  const { classes } = useStyles()
-  const session = getSession(model)
-  const [anchorEl, setAnchorEl] = useState<HTMLButtonElement | null>(null)
-
-  function handleFabClose() {
-    setAnchorEl(null)
-  }
-  const hasConnections = isSessionModelWithConnections(session)
-  const hasAddTrack = isSessionWithAddTracks(session)
-  return (
-    <>
-      {hasAddTrack || hasConnections ? (
-        <>
-          <Fab
-            color="secondary"
-            className={classes.fab}
-            onClick={event => setAnchorEl(event.currentTarget)}
-          >
-            <AddIcon />
-          </Fab>
-          <Menu
-            anchorEl={anchorEl}
-            open={Boolean(anchorEl)}
-            onClose={() => setAnchorEl(null)}
-          >
-            {hasConnections ? (
-              <MenuItem
-                onClick={() => {
-                  handleFabClose()
-                  if (isSessionModelWithWidgets(session)) {
-                    session.showWidget(
-                      session.addWidget(
-                        'AddConnectionWidget',
-                        'addConnectionWidget',
-                      ),
-                    )
-                  }
-                }}
-              >
-                Add connection
-              </MenuItem>
-            ) : null}
-            {hasAddTrack ? (
-              <MenuItem
-                onClick={() => {
-                  handleFabClose()
-                  if (isSessionModelWithWidgets(session)) {
-                    session.showWidget(
-                      session.addWidget('AddTrackWidget', 'addTrackWidget', {
-                        view: model.view.id,
-                      }),
-                    )
-                  }
-                }}
-              >
-                Add track
-              </MenuItem>
-            ) : null}
-          </Menu>
-        </>
-      ) : null}
-    </>
-  )
-})

package/src/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.test.tsx

@@ -1,148 +0,0 @@
-import React from 'react'
-import { createJBrowseTheme } from '@jbrowse/core/ui'
-import { createTestSession } from '@jbrowse/web/src/rootModel'
-import { render } from '@testing-library/react'
-import { ThemeProvider } from '@mui/material/styles'
-
-// locals
-import HierarchicalTrackSelector from './HierarchicalTrackSelector'
-
-jest.mock('@jbrowse/web/src/makeWorkerInstance', () => () => {})
-
-// @ts-expect-error
-window.requestIdleCallback = cb => cb()
-window.cancelIdleCallback = () => {}
-
-test('renders nothing with no assembly', () => {
-  const session = createTestSession()
-  const firstView = session.addView('LinearGenomeView')
-  const model = firstView.activateTrackSelector()
-
-  const { container } = render(
-    <ThemeProvider theme={createJBrowseTheme()}>
-      {/* @ts-expect-error*/}
-      <HierarchicalTrackSelector model={model} />
-    </ThemeProvider>,
-  )
-  expect(container.firstChild).toMatchSnapshot()
-})
-
-test('renders with a couple of uncategorized tracks', async () => {
-  const session = createTestSession()
-  session.addAssemblyConf({
-    name: 'volMyt1',
-    sequence: {
-      trackId: 'sequenceConfigId',
-      type: 'ReferenceSequenceTrack',
-      adapter: {
-        type: 'FromConfigSequenceAdapter',
-        features: [
-          {
-            refName: 'ctgA',
-            uniqueId: 'firstId',
-            start: 0,
-            end: 10,
-            seq: 'cattgttgcg',
-          },
-        ],
-      },
-    },
-  })
-  session.addTrackConf({
-    trackId: 'fooC',
-    assemblyNames: ['volMyt1'],
-    type: 'FeatureTrack',
-    adapter: { type: 'FromConfigAdapter', features: [] },
-  })
-  session.addTrackConf({
-    trackId: 'barC',
-    assemblyNames: ['volMyt1'],
-    type: 'FeatureTrack',
-    adapter: { type: 'FromConfigAdapter', features: [] },
-  })
-  const firstView = session.addView('LinearGenomeView', {
-    displayedRegions: [
-      {
-        assemblyName: 'volMyt1',
-        refName: 'ctgA',
-        start: 0,
-        end: 1000,
-      },
-    ],
-  })
-  firstView.showTrack(session.sessionTracks[0].trackId)
-  firstView.showTrack(session.sessionTracks[1].trackId)
-  const model = firstView.activateTrackSelector()
-
-  const { container, findByTestId } = render(
-    <ThemeProvider theme={createJBrowseTheme()}>
-      {/* @ts-expect-error*/}
-      <HierarchicalTrackSelector model={model} />
-    </ThemeProvider>,
-  )
-  await findByTestId('hierarchical_track_selector')
-  expect(container.firstChild).toMatchSnapshot()
-})
-
-test('renders with a couple of categorized tracks', async () => {
-  const session = createTestSession()
-  session.addAssemblyConf({
-    name: 'volMyt1',
-    sequence: {
-      trackId: 'sequenceConfigId',
-      type: 'ReferenceSequenceTrack',
-      adapter: {
-        type: 'FromConfigSequenceAdapter',
-        features: [
-          {
-            refName: 'ctgA',
-            uniqueId: 'firstId',
-            start: 0,
-            end: 10,
-            seq: 'cattgttgcg',
-          },
-        ],
-      },
-    },
-  })
-
-  session.addTrackConf({
-    trackId: 'fooC',
-    assemblyNames: ['volMyt1'],
-    type: 'FeatureTrack',
-    adapter: { type: 'FromConfigAdapter', features: [] },
-  })
-  session.addTrackConf({
-    trackId: 'barC',
-    assemblyNames: ['volMyt1'],
-    type: 'FeatureTrack',
-    adapter: { type: 'FromConfigAdapter', features: [] },
-  })
-  const firstView = session.addView('LinearGenomeView', {
-    displayedRegions: [
-      {
-        assemblyName: 'volMyt1',
-        refName: 'ctgA',
-        start: 0,
-        end: 1000,
-      },
-    ],
-  })
-  firstView.showTrack(session.sessionTracks[0].trackId)
-  firstView.showTrack(session.sessionTracks[1].trackId)
-  firstView.tracks[0].configuration.category.set(['Foo Category'])
-  firstView.tracks[1].configuration.category.set([
-    'Foo Category',
-    'Bar Category',
-  ])
-  const model = firstView.activateTrackSelector()
-
-  const { container, findByTestId } = render(
-    <ThemeProvider theme={createJBrowseTheme()}>
-      {/* @ts-expect-error*/}
-      <HierarchicalTrackSelector model={model} />
-    </ThemeProvider>,
-  )
-  await findByTestId('hierarchical_track_selector')
-  expect(container.firstChild).toMatchSnapshot()
-})

package/src/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.tsx

@@ -1,97 +0,0 @@
-import React, { useState } from 'react'
-import { observer } from 'mobx-react'
-import AutoSizer from 'react-virtualized-auto-sizer'
-
-// locals
-import { TreeNode, HierarchicalTrackSelectorModel } from '../model'
-import HierarchicalFab from './HierarchicalFab'
-import HierarchicalTree from './tree/HierarchicalTree'
-import HierarchicalHeader from './tree/HierarchicalHeader'
-
-// Don't use autosizer in jest and instead hardcode a height, otherwise fails
-// jest tests
-const AutoSizedHierarchicalTree = ({
-  tree,
-  model,
-  offset,
-}: {
-  tree: TreeNode
-  model: HierarchicalTrackSelectorModel
-  offset: number
-}) => {
-  return typeof jest === 'undefined' ? (
-    <AutoSizer disableWidth>
-      {({ height }) => {
-        return (
-          <HierarchicalTree
-            height={(height || offset) - offset}
-            model={model}
-            tree={tree}
-          />
-        )
-      }}
-    </AutoSizer>
-  ) : (
-    <HierarchicalTree height={9000} model={model} tree={tree} />
-  )
-}
-
-const Wrapper = ({
-  overrideDimensions,
-  children,
-}: {
-  overrideDimensions?: { width: number; height: number }
-  children: React.ReactNode
-}) => {
-  return overrideDimensions ? (
-    <div style={{ ...overrideDimensions }}>{children}</div>
-  ) : (
-    <>{children}</>
-  )
-}
-const HierarchicalTrackSelectorContainer = observer(function ({
-  model,
-  toolbarHeight,
-  overrideDimensions,
-}: {
-  model: HierarchicalTrackSelectorModel
-  toolbarHeight: number
-  overrideDimensions?: { width: number; height: number }
-}) {
-  return (
-    <Wrapper overrideDimensions={overrideDimensions}>
-      <HierarchicalTrackSelector model={model} toolbarHeight={toolbarHeight} />
-      <HierarchicalFab model={model} />
-    </Wrapper>
-  )
-})
-
-const HierarchicalTrackSelector = observer(function ({
-  model,
-  toolbarHeight = 0,
-}: {
-  model: HierarchicalTrackSelectorModel
-  toolbarHeight?: number
-}) {
-  const [assemblyIdx, setAssemblyIdx] = useState(0)
-  const [headerHeight, setHeaderHeight] = useState(0)
-
-  const { assemblyNames } = model
-  const assemblyName = assemblyNames[assemblyIdx]
-  return assemblyName ? (
-    <>
-      <HierarchicalHeader
-        model={model}
-        setHeaderHeight={setHeaderHeight}
-        setAssemblyIdx={setAssemblyIdx}
-      />
-      <AutoSizedHierarchicalTree
-        tree={model.hierarchy(assemblyName)}
-        model={model}
-        offset={toolbarHeight + headerHeight}
-      />
-    </>
-  ) : null
-})
-
-export default HierarchicalTrackSelectorContainer

package/src/HierarchicalTrackSelectorWidget/components/ShoppingCart.tsx

@@ -1,73 +0,0 @@
-import React, { useState } from 'react'
-import { Badge, IconButton } from '@mui/material'
-import { makeStyles } from 'tss-react/mui'
-import { observer } from 'mobx-react'
-import JBrowseMenu, { MenuItem } from '@jbrowse/core/ui/Menu'
-import { getSession, getEnv } from '@jbrowse/core/util'
-
-// icons
-import ShoppingCartIcon from '@mui/icons-material/ShoppingCart'
-
-// locals
-import { HierarchicalTrackSelectorModel } from '../model'
-
-const useStyles = makeStyles()(theme => ({
-  searchBox: {
-    margin: theme.spacing(2),
-  },
-  menuIcon: {
-    marginRight: theme.spacing(1),
-    marginBottom: 0,
-  },
-}))
-
-export default observer(function ShoppingCart({
-  model,
-}: {
-  model: HierarchicalTrackSelectorModel
-}) {
-  const { classes } = useStyles()
-  const { selection } = model
-  const { pluginManager } = getEnv(model)
-  const session = getSession(model)
-  const [selectionEl, setSelectionEl] = useState<HTMLButtonElement>()
-  const items = pluginManager.evaluateExtensionPoint(
-    'TrackSelector-multiTrackMenuItems',
-    [],
-    { session },
-  ) as MenuItem[]
-
-  return (
-    <>
-      {selection.length ? (
-        <IconButton
-          className={classes.menuIcon}
-          onClick={event => setSelectionEl(event.currentTarget)}
-        >
-          <Badge badgeContent={selection.length} color="primary">
-            <ShoppingCartIcon />
-          </Badge>
-        </IconButton>
-      ) : null}
-
-      <JBrowseMenu
-        anchorEl={selectionEl}
-        open={Boolean(selectionEl)}
-        onMenuItemClick={(_, callback) => {
-          callback()
-          setSelectionEl(undefined)
-        }}
-        onClose={() => setSelectionEl(undefined)}
-        menuItems={[
-          { label: 'Clear', onClick: () => model.clearSelection() },
-          ...items.map(item => ({
-            ...item,
-            ...('onClick' in item
-              ? { onClick: () => item.onClick(model) }
-              : {}),
-          })),
-        ]}
-      />
-    </>
-  )
-})