@jbrowse/plugin-data-management 2.6.1 → 2.6.2

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

@@ -1,265 +0,0 @@
-// Jest Snapshot v1, https://goo.gl/fbAQLP
-
-exports[`renders nothing with no assembly 1`] = `
-<div
-  data-testid="hierarchical_track_selector"
->
-  <div
-    style="display: flex;"
-  >
-    <button
-      class="MuiButtonBase-root MuiIconButton-root MuiIconButton-sizeSmall css-1kgqocu-MuiButtonBase-root-MuiIconButton-root-menuIcon"
-      tabindex="0"
-      type="button"
-    >
-      <svg
-        aria-hidden="true"
-        class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-havevq-MuiSvgIcon-root"
-        data-testid="MenuIcon"
-        focusable="false"
-        viewBox="0 0 24 24"
-      >
-        <path
-          d="M3 18h18v-2H3v2zm0-5h18v-2H3v2zm0-7v2h18V6H3z"
-        />
-      </svg>
-      <span
-        class="MuiTouchRipple-root css-8je8zh-MuiTouchRipple-root"
-      />
-    </button>
-    <div
-      class="MuiFormControl-root MuiFormControl-marginDense MuiFormControl-fullWidth MuiTextField-root css-rlnh8o-MuiFormControl-root-MuiTextField-root-searchBox"
-    >
-      <label
-        class="MuiFormLabel-root MuiInputLabel-root MuiInputLabel-formControl MuiInputLabel-animated MuiInputLabel-sizeSmall MuiInputLabel-standard MuiFormLabel-colorPrimary MuiInputLabel-root MuiInputLabel-formControl MuiInputLabel-animated MuiInputLabel-sizeSmall MuiInputLabel-standard css-1s1jvl0-MuiFormLabel-root-MuiInputLabel-root"
-        data-shrink="false"
-        for="mui-1"
-        id="mui-1-label"
-      >
-        Filter tracks
-      </label>
-      <div
-        class="MuiInputBase-root MuiInput-root MuiInput-underline MuiInputBase-colorPrimary MuiInputBase-fullWidth MuiInputBase-formControl MuiInputBase-sizeSmall MuiInputBase-adornedEnd css-1blad95-MuiInputBase-root-MuiInput-root"
-      >
-        <input
-          aria-invalid="false"
-          class="MuiInputBase-input MuiInput-input MuiInputBase-inputSizeSmall MuiInputBase-inputAdornedEnd css-nz481w-MuiInputBase-input-MuiInput-input"
-          id="mui-1"
-          type="text"
-          value=""
-        />
-        <div
-          class="MuiInputAdornment-root MuiInputAdornment-positionEnd MuiInputAdornment-standard MuiInputAdornment-sizeSmall css-1laqsz7-MuiInputAdornment-root"
-        >
-          <button
-            class="MuiButtonBase-root MuiIconButton-root MuiIconButton-sizeSmall css-9vna8i-MuiButtonBase-root-MuiIconButton-root"
-            tabindex="0"
-            type="button"
-          >
-            <svg
-              aria-hidden="true"
-              class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-havevq-MuiSvgIcon-root"
-              data-testid="ClearIcon"
-              focusable="false"
-              viewBox="0 0 24 24"
-            >
-              <path
-                d="M19 6.41 17.59 5 12 10.59 6.41 5 5 6.41 10.59 12 5 17.59 6.41 19 12 13.41 17.59 19 19 17.59 13.41 12z"
-              />
-            </svg>
-            <span
-              class="MuiTouchRipple-root css-8je8zh-MuiTouchRipple-root"
-            />
-          </button>
-        </div>
-      </div>
-    </div>
-    <button
-      class="MuiButtonBase-root MuiButton-root MuiButton-text MuiButton-textPrimary MuiButton-sizeSmall MuiButton-textSizeSmall MuiButton-root MuiButton-text MuiButton-textPrimary MuiButton-sizeSmall MuiButton-textSizeSmall css-1c8zr45-MuiButtonBase-root-MuiButton-root-menuIcon"
-      tabindex="0"
-      type="button"
-    >
-      Open faceted selector
-      <span
-        class="MuiTouchRipple-root css-8je8zh-MuiTouchRipple-root"
-      />
-    </button>
-  </div>
-</div>
-`;
-
-exports[`renders with a couple of categorized tracks 1`] = `
-<div
-  data-testid="hierarchical_track_selector"
->
-  <div
-    style="display: flex;"
-  >
-    <button
-      class="MuiButtonBase-root MuiIconButton-root MuiIconButton-sizeSmall css-1kgqocu-MuiButtonBase-root-MuiIconButton-root-menuIcon"
-      tabindex="0"
-      type="button"
-    >
-      <svg
-        aria-hidden="true"
-        class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-havevq-MuiSvgIcon-root"
-        data-testid="MenuIcon"
-        focusable="false"
-        viewBox="0 0 24 24"
-      >
-        <path
-          d="M3 18h18v-2H3v2zm0-5h18v-2H3v2zm0-7v2h18V6H3z"
-        />
-      </svg>
-      <span
-        class="MuiTouchRipple-root css-8je8zh-MuiTouchRipple-root"
-      />
-    </button>
-    <div
-      class="MuiFormControl-root MuiFormControl-marginDense MuiFormControl-fullWidth MuiTextField-root css-rlnh8o-MuiFormControl-root-MuiTextField-root-searchBox"
-    >
-      <label
-        class="MuiFormLabel-root MuiInputLabel-root MuiInputLabel-formControl MuiInputLabel-animated MuiInputLabel-sizeSmall MuiInputLabel-standard MuiFormLabel-colorPrimary MuiInputLabel-root MuiInputLabel-formControl MuiInputLabel-animated MuiInputLabel-sizeSmall MuiInputLabel-standard css-1s1jvl0-MuiFormLabel-root-MuiInputLabel-root"
-        data-shrink="false"
-        for="mui-6"
-        id="mui-6-label"
-      >
-        Filter tracks
-      </label>
-      <div
-        class="MuiInputBase-root MuiInput-root MuiInput-underline MuiInputBase-colorPrimary MuiInputBase-fullWidth MuiInputBase-formControl MuiInputBase-sizeSmall MuiInputBase-adornedEnd css-1blad95-MuiInputBase-root-MuiInput-root"
-      >
-        <input
-          aria-invalid="false"
-          class="MuiInputBase-input MuiInput-input MuiInputBase-inputSizeSmall MuiInputBase-inputAdornedEnd css-nz481w-MuiInputBase-input-MuiInput-input"
-          id="mui-6"
-          type="text"
-          value=""
-        />
-        <div
-          class="MuiInputAdornment-root MuiInputAdornment-positionEnd MuiInputAdornment-standard MuiInputAdornment-sizeSmall css-1laqsz7-MuiInputAdornment-root"
-        >
-          <button
-            class="MuiButtonBase-root MuiIconButton-root MuiIconButton-sizeSmall css-9vna8i-MuiButtonBase-root-MuiIconButton-root"
-            tabindex="0"
-            type="button"
-          >
-            <svg
-              aria-hidden="true"
-              class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-havevq-MuiSvgIcon-root"
-              data-testid="ClearIcon"
-              focusable="false"
-              viewBox="0 0 24 24"
-            >
-              <path
-                d="M19 6.41 17.59 5 12 10.59 6.41 5 5 6.41 10.59 12 5 17.59 6.41 19 12 13.41 17.59 19 19 17.59 13.41 12z"
-              />
-            </svg>
-            <span
-              class="MuiTouchRipple-root css-8je8zh-MuiTouchRipple-root"
-            />
-          </button>
-        </div>
-      </div>
-    </div>
-    <button
-      class="MuiButtonBase-root MuiButton-root MuiButton-text MuiButton-textPrimary MuiButton-sizeSmall MuiButton-textSizeSmall MuiButton-root MuiButton-text MuiButton-textPrimary MuiButton-sizeSmall MuiButton-textSizeSmall css-1c8zr45-MuiButtonBase-root-MuiButton-root-menuIcon"
-      tabindex="0"
-      type="button"
-    >
-      Open faceted selector
-      <span
-        class="MuiTouchRipple-root css-8je8zh-MuiTouchRipple-root"
-      />
-    </button>
-  </div>
-</div>
-`;
-
-exports[`renders with a couple of uncategorized tracks 1`] = `
-<div
-  data-testid="hierarchical_track_selector"
->
-  <div
-    style="display: flex;"
-  >
-    <button
-      class="MuiButtonBase-root MuiIconButton-root MuiIconButton-sizeSmall css-1kgqocu-MuiButtonBase-root-MuiIconButton-root-menuIcon"
-      tabindex="0"
-      type="button"
-    >
-      <svg
-        aria-hidden="true"
-        class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-havevq-MuiSvgIcon-root"
-        data-testid="MenuIcon"
-        focusable="false"
-        viewBox="0 0 24 24"
-      >
-        <path
-          d="M3 18h18v-2H3v2zm0-5h18v-2H3v2zm0-7v2h18V6H3z"
-        />
-      </svg>
-      <span
-        class="MuiTouchRipple-root css-8je8zh-MuiTouchRipple-root"
-      />
-    </button>
-    <div
-      class="MuiFormControl-root MuiFormControl-marginDense MuiFormControl-fullWidth MuiTextField-root css-rlnh8o-MuiFormControl-root-MuiTextField-root-searchBox"
-    >
-      <label
-        class="MuiFormLabel-root MuiInputLabel-root MuiInputLabel-formControl MuiInputLabel-animated MuiInputLabel-sizeSmall MuiInputLabel-standard MuiFormLabel-colorPrimary MuiInputLabel-root MuiInputLabel-formControl MuiInputLabel-animated MuiInputLabel-sizeSmall MuiInputLabel-standard css-1s1jvl0-MuiFormLabel-root-MuiInputLabel-root"
-        data-shrink="false"
-        for="mui-2"
-        id="mui-2-label"
-      >
-        Filter tracks
-      </label>
-      <div
-        class="MuiInputBase-root MuiInput-root MuiInput-underline MuiInputBase-colorPrimary MuiInputBase-fullWidth MuiInputBase-formControl MuiInputBase-sizeSmall MuiInputBase-adornedEnd css-1blad95-MuiInputBase-root-MuiInput-root"
-      >
-        <input
-          aria-invalid="false"
-          class="MuiInputBase-input MuiInput-input MuiInputBase-inputSizeSmall MuiInputBase-inputAdornedEnd css-nz481w-MuiInputBase-input-MuiInput-input"
-          id="mui-2"
-          type="text"
-          value=""
-        />
-        <div
-          class="MuiInputAdornment-root MuiInputAdornment-positionEnd MuiInputAdornment-standard MuiInputAdornment-sizeSmall css-1laqsz7-MuiInputAdornment-root"
-        >
-          <button
-            class="MuiButtonBase-root MuiIconButton-root MuiIconButton-sizeSmall css-9vna8i-MuiButtonBase-root-MuiIconButton-root"
-            tabindex="0"
-            type="button"
-          >
-            <svg
-              aria-hidden="true"
-              class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-havevq-MuiSvgIcon-root"
-              data-testid="ClearIcon"
-              focusable="false"
-              viewBox="0 0 24 24"
-            >
-              <path
-                d="M19 6.41 17.59 5 12 10.59 6.41 5 5 6.41 10.59 12 5 17.59 6.41 19 12 13.41 17.59 19 19 17.59 13.41 12z"
-              />
-            </svg>
-            <span
-              class="MuiTouchRipple-root css-8je8zh-MuiTouchRipple-root"
-            />
-          </button>
-        </div>
-      </div>
-    </div>
-    <button
-      class="MuiButtonBase-root MuiButton-root MuiButton-text MuiButton-textPrimary MuiButton-sizeSmall MuiButton-textSizeSmall MuiButton-root MuiButton-text MuiButton-textPrimary MuiButton-sizeSmall MuiButton-textSizeSmall css-1c8zr45-MuiButtonBase-root-MuiButton-root-menuIcon"
-      tabindex="0"
-      type="button"
-    >
-      Open faceted selector
-      <span
-        class="MuiTouchRipple-root css-8je8zh-MuiTouchRipple-root"
-      />
-    </button>
-  </div>
-</div>
-`;

package/src/HierarchicalTrackSelectorWidget/components/dialogs/CloseConnectionDialog.tsx

@@ -1,65 +0,0 @@
-import React from 'react'
-import {
-  DialogContent,
-  DialogContentText,
-  Button,
-  List,
-  ListItem,
-  DialogActions,
-} from '@mui/material'
-import { Dialog } from '@jbrowse/core/ui'
-import { observer } from 'mobx-react'
-
-export default observer(function CloseConnectionDialog({
-  modalInfo = {},
-  onClose,
-}: {
-  modalInfo?: {
-    name?: string
-    dereferenceTypeCount?: { [key: string]: number }
-    safelyBreakConnection?: () => void
-  }
-  onClose: () => void
-}) {
-  const { name, dereferenceTypeCount, safelyBreakConnection } = modalInfo
-  return (
-    <Dialog open maxWidth="lg" title={`Close connection "${name}"`}>
-      <DialogContent>
-        {dereferenceTypeCount ? (
-          <>
-            <DialogContentText>
-              Closing this connection will close:
-            </DialogContentText>
-            <List>
-              {Object.entries(dereferenceTypeCount).map(([key, value]) => (
-                <ListItem key={key}>{`${value} ${key}`}</ListItem>
-              ))}
-            </List>
-          </>
-        ) : null}
-        <DialogContentText>
-          Are you sure you want to close this connection?
-        </DialogContentText>
-      </DialogContent>
-      <DialogActions>
-        <Button onClick={() => onClose()} color="primary">
-          Cancel
-        </Button>
-        <Button
-          variant="contained"
-          onClick={
-            modalInfo
-              ? () => {
-                  safelyBreakConnection?.()
-                  onClose()
-                }
-              : () => {}
-          }
-          color="primary"
-        >
-          OK
-        </Button>
-      </DialogActions>
-    </Dialog>
-  )
-})

package/src/HierarchicalTrackSelectorWidget/components/dialogs/DeleteConnectionDialog.tsx

@@ -1,53 +0,0 @@
-import React from 'react'
-import {
-  Dialog,
-  DialogTitle,
-  DialogContent,
-  DialogContentText,
-  DialogActions,
-  Button,
-} from '@mui/material'
-import { observer } from 'mobx-react'
-import { AnyConfigurationModel } from '@jbrowse/core/configuration'
-import { AbstractSessionModel } from '@jbrowse/core/util'
-
-function DeleteConnectionDialog({
-  deleteDialogDetails,
-  session,
-  handleClose,
-}: {
-  deleteDialogDetails: { name: string; connectionConf: AnyConfigurationModel }
-  session: AbstractSessionModel
-  handleClose: () => void
-}) {
-  const { connectionConf, name } = deleteDialogDetails
-  return (
-    <Dialog open>
-      <DialogTitle>Delete connection &quot;{name}&quot;</DialogTitle>
-      <DialogContent>
-        <DialogContentText>
-          Are you sure you want to delete this connection?
-        </DialogContentText>
-      </DialogContent>
-      <DialogActions>
-        <Button onClick={() => handleClose()} color="primary">
-          Cancel
-        </Button>
-        <Button
-          variant="contained"
-          color="primary"
-          onClick={() => {
-            if (connectionConf) {
-              session.deleteConnection?.(connectionConf)
-            }
-            handleClose()
-          }}
-        >
-          OK
-        </Button>
-      </DialogActions>
-    </Dialog>
-  )
-}
-
-export default observer(DeleteConnectionDialog)

package/src/HierarchicalTrackSelectorWidget/components/dialogs/ManageConnectionsDialog.tsx

@@ -1,84 +0,0 @@
-import React from 'react'
-import {
-  Button,
-  DialogContent,
-  DialogActions,
-  IconButton,
-  Tooltip,
-  Typography,
-} from '@mui/material'
-import { Dialog } from '@jbrowse/core/ui'
-import { makeStyles } from 'tss-react/mui'
-import { observer } from 'mobx-react'
-import {
-  AnyConfigurationModel,
-  readConfObject,
-} from '@jbrowse/core/configuration'
-import { AbstractSessionModel } from '@jbrowse/core/util'
-
-// icons
-import CloseIcon from '@mui/icons-material/Close'
-
-const useStyles = makeStyles()(theme => ({
-  connectionContainer: {
-    margin: theme.spacing(4),
-    width: 500,
-  },
-}))
-
-function ManageConnectionsDlg({
-  session,
-  handleClose,
-  breakConnection,
-}: {
-  handleClose: () => void
-  session: AbstractSessionModel
-  breakConnection: (conf: AnyConfigurationModel, arg: boolean) => void
-}) {
-  const { classes } = useStyles()
-  const { adminMode, connections, sessionConnections } = session
-  return (
-    <Dialog open onClose={handleClose} maxWidth="lg" title="Delete connections">
-      <DialogContent>
-        <Typography>
-          Click the X icon to delete the connection from your config completely
-        </Typography>
-        <div className={classes.connectionContainer}>
-          {connections.map(conf => {
-            const name = readConfObject(conf, 'name')
-            return (
-              <Typography key={`conn-${name}`}>
-                {adminMode || sessionConnections?.includes(conf) ? (
-                  <IconButton onClick={() => breakConnection(conf, true)}>
-                    <CloseIcon color="error" />
-                  </IconButton>
-                ) : (
-                  <Tooltip title="Unable to delete connection in config file as non-admin user">
-                    <IconButton>
-                      <CloseIcon color="disabled" />
-                    </IconButton>
-                  </Tooltip>
-                )}
-                {name}
-              </Typography>
-            )
-          })}
-          {!connections.length ? (
-            <Typography>No connections found</Typography>
-          ) : null}
-        </div>
-      </DialogContent>
-      <DialogActions>
-        <Button
-          onClick={() => handleClose()}
-          variant="contained"
-          color="primary"
-        >
-          Close
-        </Button>
-      </DialogActions>
-    </Dialog>
-  )
-}
-
-export default observer(ManageConnectionsDlg)

package/src/HierarchicalTrackSelectorWidget/components/dialogs/ToggleConnectionsDialog.tsx

@@ -1,127 +0,0 @@
-import React from 'react'
-import {
-  Button,
-  Checkbox,
-  DialogContent,
-  DialogActions,
-  FormControlLabel,
-  Typography,
-} from '@mui/material'
-import { Dialog } from '@jbrowse/core/ui'
-import { makeStyles } from 'tss-react/mui'
-import { observer } from 'mobx-react'
-import {
-  AnyConfigurationModel,
-  readConfObject,
-} from '@jbrowse/core/configuration'
-import { AbstractSessionModel } from '@jbrowse/core/util'
-
-export function ellipses(slug: string) {
-  return slug.length > 20 ? `${slug.slice(0, 20)}...` : slug
-}
-
-const useStyles = makeStyles()(theme => ({
-  connectionContainer: {
-    width: 500,
-    margin: theme.spacing(4),
-  },
-}))
-
-const ConnectionRow = observer(function ConnectionRow({
-  conf,
-  session,
-  breakConnection,
-}: {
-  conf: AnyConfigurationModel
-  session: AbstractSessionModel
-  breakConnection: (arg: AnyConfigurationModel) => void
-}) {
-  const { connectionInstances: instances = [] } = session
-  const name = readConfObject(conf, 'name')
-  const assemblyNames = readConfObject(conf, 'assemblyNames')
-  const found = instances.find(conn => name === conn.name)
-  return (
-    <FormControlLabel
-      key={conf.connectionId}
-      control={
-        <Checkbox
-          checked={!!found}
-          onChange={() => {
-            if (found) {
-              breakConnection(conf)
-            } else {
-              session.makeConnection?.(conf)
-            }
-          }}
-          color="primary"
-        />
-      }
-      label={[
-        name,
-        assemblyNames.length ? `(${ellipses(assemblyNames.join(','))})` : '',
-      ]
-        .filter(f => !!f)
-        .join(' ')}
-    />
-  )
-})
-
-const ConnectionList = observer(function ConnectionsList({
-  session,
-  breakConnection,
-}: {
-  session: AbstractSessionModel
-  breakConnection: (arg: AnyConfigurationModel) => void
-}) {
-  const { classes } = useStyles()
-  return (
-    <div className={classes.connectionContainer}>
-      {!session.connections.length ? (
-        <Typography>No connections found</Typography>
-      ) : (
-        session.connections.map((conf, idx) => (
-          <div key={conf.name + '_' + idx}>
-            <ConnectionRow
-              conf={conf}
-              session={session}
-              breakConnection={breakConnection}
-            />
-          </div>
-        ))
-      )}
-    </div>
-  )
-})
-
-export default observer(function ToggleConnectionDialog({
-  session,
-  handleClose,
-  breakConnection,
-}: {
-  handleClose: () => void
-  session: AbstractSessionModel
-  breakConnection: (arg: AnyConfigurationModel) => void
-}) {
-  return (
-    <Dialog
-      open
-      onClose={handleClose}
-      maxWidth="lg"
-      title="Turn on/off connections"
-    >
-      <DialogContent>
-        <Typography>Use the checkbox to turn on/off connections</Typography>
-        <ConnectionList session={session} breakConnection={breakConnection} />
-      </DialogContent>
-      <DialogActions>
-        <Button
-          onClick={() => handleClose()}
-          variant="contained"
-          color="primary"
-        >
-          Close
-        </Button>
-      </DialogActions>
-    </Dialog>
-  )
-})