@jbrowse/plugin-data-management 2.3.3 → 2.3.4

package/esm/HierarchicalTrackSelectorWidget/components/Node.js

@@ -1,144 +0,0 @@
-import React, { useState } from 'react';
-import { Checkbox, FormControlLabel, IconButton, Tooltip, Typography, } from '@mui/material';
-import { makeStyles } from 'tss-react/mui';
-// icons
-import ArrowDropDownIcon from '@mui/icons-material/ArrowDropDown';
-import ArrowRightIcon from '@mui/icons-material/ArrowRight';
-import MoreHorizIcon from '@mui/icons-material/MoreHoriz';
-import JBrowseMenu from '@jbrowse/core/ui/Menu';
-import { getSession } from '@jbrowse/core/util';
-import { readConfObject, } from '@jbrowse/core/configuration';
-import { getAllChildren } from './util';
-const useStyles = makeStyles()(theme => ({
-    compactCheckbox: {
-        padding: 0,
-    },
-    checkboxLabel: {
-        marginRight: 0,
-        '&:hover': {
-            backgroundColor: '#eee',
-        },
-    },
-    contrastColor: {
-        color: theme.palette.secondary.contrastText,
-    },
-    // this accordionBase element's small padding is used to give a margin to
-    // accordionColor it a "margin" because the virtualized elements can't really
-    // use margin in a conventional way (it doesn't affect layout)
-    accordionBase: {
-        display: 'flex',
-    },
-    accordionCard: {
-        padding: 3,
-        cursor: 'pointer',
-        display: 'flex',
-    },
-    nestingLevelMarker: {
-        position: 'absolute',
-        borderLeft: '1.5px solid #555',
-    },
-    // accordionColor set's display:flex so that the child accordionText use
-    // vertically centered text
-    accordionColor: {
-        background: theme.palette.tertiary.main,
-        color: theme.palette.tertiary.contrastText,
-        width: '100%',
-        display: 'flex',
-        paddingLeft: 5,
-    },
-    // margin:auto 0 to center text vertically
-    accordionText: {
-        margin: 'auto 0',
-    },
-}));
-function treeToMap(tree, map = new Map()) {
-    if (tree.id && tree.children.length) {
-        map.set(tree.id, tree);
-    }
-    for (let i = 0; i < tree.children.length; i++) {
-        const node = tree.children[i];
-        treeToMap(node, map);
-    }
-    return map;
-}
-function isUnsupported(name = '') {
-    return name.endsWith('(Unsupported)') || name.endsWith('(Unknown)');
-}
-// An individual node in the track selector. Note: manually sets cursor:
-// pointer improves usability for what can be clicked
-export default function Node(props) {
-    var _a, _b;
-    const { data, isOpen, style, setOpen } = props;
-    const { checked, conf, drawerPosition, id, isLeaf, model, name, nestingLevel, onChange, selected, toggleCollapse, tree, } = data;
-    const { classes } = useStyles();
-    const width = 10;
-    const [menuEl, setMenuEl] = useState(null);
-    const [info, setInfo] = useState();
-    const marginLeft = nestingLevel * width + (isLeaf ? width : 0);
-    const description = (conf && readConfObject(conf, ['description'])) || '';
-    return (React.createElement("div", { style: style, className: !isLeaf ? classes.accordionBase : undefined },
-        new Array(nestingLevel).fill(0).map((_, idx) => (React.createElement("div", { key: `mark-${idx}`, style: { left: idx * width + 4, height: style === null || style === void 0 ? void 0 : style.height }, className: classes.nestingLevelMarker }))),
-        React.createElement("div", { className: !isLeaf ? classes.accordionCard : undefined, onClick: () => {
-                if (!menuEl) {
-                    toggleCollapse(id);
-                    setOpen(!isOpen);
-                }
-            }, style: {
-                marginLeft,
-                whiteSpace: 'nowrap',
-                width: '100%',
-            } },
-            React.createElement("div", { className: !isLeaf ? classes.accordionColor : undefined },
-                !isLeaf ? (React.createElement("div", { className: classes.accordionText },
-                    React.createElement(Typography, null,
-                        isOpen ? React.createElement(ArrowDropDownIcon, null) : React.createElement(ArrowRightIcon, null),
-                        name,
-                        React.createElement(IconButton, { onClick: event => {
-                                setMenuEl(event.currentTarget);
-                                event.stopPropagation();
-                            }, className: classes.contrastColor },
-                            React.createElement(MoreHorizIcon, null))))) : (React.createElement(React.Fragment, null,
-                    React.createElement(Tooltip, { title: description + (selected ? ' (in selection)' : ''), placement: drawerPosition === 'left' ? 'right' : 'left' },
-                        React.createElement(FormControlLabel, { className: classes.checkboxLabel, control: React.createElement(Checkbox, { className: classes.compactCheckbox, checked: checked, onChange: () => onChange(id), disabled: isUnsupported(name), inputProps: {
-                                    // @ts-ignore
-                                    'data-testid': `htsTrackEntry-${id}`,
-                                } }), label: React.createElement("div", { style: {
-                                    background: selected ? '#cccc' : undefined,
-                                    padding: 1,
-                                } }, name) })),
-                    React.createElement(IconButton, { onClick: e => setInfo({ target: e.currentTarget, id, conf }), style: { padding: 0 }, color: "secondary", "data-testid": `htsTrackEntryMenu-${id}` },
-                        React.createElement(MoreHorizIcon, null)))),
-                menuEl ? (React.createElement(JBrowseMenu, { anchorEl: menuEl, menuItems: [
-                        {
-                            label: 'Add to selection',
-                            onClick: () => model.addToSelection(getAllChildren(treeToMap(tree).get(id))),
-                        },
-                        {
-                            label: 'Remove from selection',
-                            onClick: () => model.removeFromSelection(getAllChildren(treeToMap(tree).get(id))),
-                        },
-                    ], onMenuItemClick: (_event, callback) => {
-                        callback();
-                        setMenuEl(null);
-                    }, open: Boolean(menuEl), onClose: () => setMenuEl(null) })) : null,
-                info ? (React.createElement(JBrowseMenu, { anchorEl: info === null || info === void 0 ? void 0 : info.target, menuItems: [
-                        ...(((_b = (_a = getSession(model)).getTrackActionMenuItems) === null || _b === void 0 ? void 0 : _b.call(_a, info.conf)) ||
-                            []),
-                        {
-                            label: 'Add to selection',
-                            onClick: () => model.addToSelection([info.conf]),
-                        },
-                        ...(selected
-                            ? [
-                                {
-                                    label: 'Remove from selection',
-                                    onClick: () => model.removeFromSelection([info.conf]),
-                                },
-                            ]
-                            : []),
-                    ], onMenuItemClick: (_event, callback) => {
-                        callback();
-                        setInfo(undefined);
-                    }, open: Boolean(info), onClose: () => setInfo(undefined) })) : null))));
-}
-//# sourceMappingURL=Node.js.map

package/esm/HierarchicalTrackSelectorWidget/components/Node.js.map

@@ -1 +0,0 @@
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package/esm/HierarchicalTrackSelectorWidget/components/ToggleConnectionsDialog.js.map

@@ -1 +0,0 @@
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package/src/HierarchicalTrackSelectorWidget/components/Header.tsx

@@ -1,286 +0,0 @@
-import React, { Suspense, lazy, useState } from 'react'
-import { Badge, IconButton, InputAdornment, TextField } 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,
-  isSessionModelWithWidgets,
-  isSessionModelWithConnections,
-  isSessionWithAddTracks,
-} from '@jbrowse/core/util'
-import {
-  AnyConfigurationModel,
-  readConfObject,
-} from '@jbrowse/core/configuration'
-
-// icons
-import ClearIcon from '@mui/icons-material/Clear'
-import MenuIcon from '@mui/icons-material/Menu'
-import ShoppingCartIcon from '@mui/icons-material/ShoppingCart'
-import { Cable } from '@jbrowse/core/ui/Icons'
-
-// locals
-import { HierarchicalTrackSelectorModel } from '../model'
-
-// lazy components
-const CloseConnectionDialog = lazy(() => import('./CloseConnectionDialog'))
-const DeleteConnectionDialog = lazy(() => import('./DeleteConnectionDialog'))
-const ManageConnectionsDialog = lazy(() => import('./ManageConnectionsDialog'))
-const ToggleConnectionsDialog = lazy(() => import('./ToggleConnectionsDialog'))
-
-const useStyles = makeStyles()(theme => ({
-  searchBox: {
-    margin: theme.spacing(2),
-  },
-  menuIcon: {
-    marginRight: theme.spacing(1),
-    marginBottom: 0,
-  },
-}))
-
-interface ModalArgs {
-  connectionConf: AnyConfigurationModel
-  safelyBreakConnection: Function
-  dereferenceTypeCount: { [key: string]: number }
-  name: string
-}
-
-interface DialogDetails {
-  name: string
-  connectionConf: AnyConfigurationModel
-}
-
-function HierarchicalTrackSelectorHeader({
-  model,
-  setHeaderHeight,
-  setAssemblyIdx,
-  assemblyIdx,
-}: {
-  model: HierarchicalTrackSelectorModel
-  setHeaderHeight: (n: number) => void
-  setAssemblyIdx: (n: number) => void
-  assemblyIdx: number
-}) {
-  const { classes } = useStyles()
-  const session = getSession(model)
-  const [connectionEl, setConnectionEl] = useState<HTMLButtonElement>()
-  const [selectionEl, setSelectionEl] = useState<HTMLButtonElement>()
-  const [menuEl, setMenuEl] = useState<HTMLButtonElement>()
-  const [modalInfo, setModalInfo] = useState<ModalArgs>()
-  const [deleteDlgDetails, setDeleteDlgDetails] = useState<DialogDetails>()
-  const [connectionManagerOpen, setConnectionManagerOpen] = useState(false)
-  const [connectionToggleOpen, setConnectionToggleOpen] = useState(false)
-  const { assemblyNames } = model
-
-  function breakConnection(
-    connectionConf: AnyConfigurationModel,
-    deletingConnection?: boolean,
-  ) {
-    const name = readConfObject(connectionConf, 'name')
-
-    // @ts-ignore
-    const result = session.prepareToBreakConnection(connectionConf)
-    if (result) {
-      const [safelyBreakConnection, dereferenceTypeCount] = result
-      if (Object.keys(dereferenceTypeCount).length > 0) {
-        setModalInfo({
-          connectionConf,
-          safelyBreakConnection,
-          dereferenceTypeCount,
-          name,
-        })
-      } else {
-        safelyBreakConnection()
-      }
-    }
-    if (deletingConnection) {
-      setDeleteDlgDetails({ name, connectionConf })
-    }
-  }
-
-  const connectionMenuItems = [
-    {
-      label: 'Turn on/off connections...',
-      onClick: () => setConnectionToggleOpen(true),
-    },
-  ]
-
-  if (isSessionModelWithConnections(session)) {
-    connectionMenuItems.unshift({
-      label: 'Add connection',
-      onClick: () => {
-        if (isSessionModelWithWidgets(session)) {
-          session.showWidget(
-            session.addWidget('AddConnectionWidget', 'addConnectionWidget'),
-          )
-        }
-      },
-    })
-
-    connectionMenuItems.push({
-      label: 'Delete connections...',
-      onClick: () => setConnectionManagerOpen(true),
-    })
-  }
-
-  const assemblyMenuItems =
-    assemblyNames.length > 1
-      ? [
-          {
-            label: 'Select assembly...',
-            subMenu: assemblyNames.map((name, idx) => ({
-              label: name,
-              onClick: () => setAssemblyIdx(idx),
-            })),
-          },
-        ]
-      : []
-
-  const menuItems = [
-    {
-      label: 'Add track...',
-      onClick: () => {
-        if (isSessionModelWithWidgets(session)) {
-          session.showWidget(
-            session.addWidget('AddTrackWidget', 'addTrackWidget', {
-              view: model.view.id,
-            }),
-          )
-        }
-      },
-    },
-
-    ...assemblyMenuItems,
-  ]
-
-  const items = getEnv(model).pluginManager.evaluateExtensionPoint(
-    'TrackSelector-multiTrackMenuItems',
-    [],
-    { session },
-  ) as MenuItem[]
-  return (
-    <div
-      ref={ref => setHeaderHeight(ref?.getBoundingClientRect().height || 0)}
-      data-testid="hierarchical_track_selector"
-    >
-      <div style={{ display: 'flex' }}>
-        {isSessionWithAddTracks(session) && (
-          <IconButton
-            className={classes.menuIcon}
-            onClick={event => setMenuEl(event.currentTarget)}
-          >
-            <MenuIcon />
-          </IconButton>
-        )}
-
-        {session.makeConnection && (
-          <IconButton
-            className={classes.menuIcon}
-            onClick={event => setConnectionEl(event.currentTarget)}
-          >
-            <Cable />
-          </IconButton>
-        )}
-
-        {model.selection.length ? (
-          <IconButton
-            className={classes.menuIcon}
-            onClick={event => setSelectionEl(event.currentTarget)}
-          >
-            <Badge badgeContent={model.selection.length} color="primary">
-              <ShoppingCartIcon />
-            </Badge>
-          </IconButton>
-        ) : null}
-
-        <TextField
-          className={classes.searchBox}
-          label="Filter tracks"
-          value={model.filterText}
-          onChange={event => model.setFilterText(event.target.value)}
-          fullWidth
-          InputProps={{
-            endAdornment: (
-              <InputAdornment position="end">
-                <IconButton color="secondary" onClick={model.clearFilterText}>
-                  <ClearIcon />
-                </IconButton>
-              </InputAdornment>
-            ),
-          }}
-        />
-      </div>
-      <JBrowseMenu
-        anchorEl={connectionEl}
-        open={Boolean(connectionEl)}
-        onMenuItemClick={(_, callback) => {
-          callback()
-          setConnectionEl(undefined)
-        }}
-        onClose={() => setConnectionEl(undefined)}
-        menuItems={connectionMenuItems}
-      />
-      <JBrowseMenu
-        anchorEl={menuEl}
-        open={Boolean(menuEl)}
-        onMenuItemClick={(_, callback) => {
-          callback()
-          setMenuEl(undefined)
-        }}
-        onClose={() => setMenuEl(undefined)}
-        menuItems={menuItems}
-      />
-      <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) }
-              : {}),
-          })),
-        ]}
-      />
-      <Suspense fallback={<div />}>
-        {modalInfo ? (
-          <CloseConnectionDialog
-            modalInfo={modalInfo}
-            setModalInfo={setModalInfo}
-          />
-        ) : null}
-        {deleteDlgDetails ? (
-          <DeleteConnectionDialog
-            handleClose={() => setDeleteDlgDetails(undefined)}
-            deleteDialogDetails={deleteDlgDetails}
-            session={session}
-          />
-        ) : null}
-        {connectionManagerOpen ? (
-          <ManageConnectionsDialog
-            handleClose={() => setConnectionManagerOpen(false)}
-            breakConnection={breakConnection}
-            session={session}
-          />
-        ) : null}
-        {connectionToggleOpen ? (
-          <ToggleConnectionsDialog
-            handleClose={() => setConnectionToggleOpen(false)}
-            session={session}
-            breakConnection={breakConnection}
-          />
-        ) : null}
-      </Suspense>
-    </div>
-  )
-}
-
-export default observer(HierarchicalTrackSelectorHeader)