@jbrowse/plugin-data-management 2.7.0 → 2.7.1

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Files changed (11) hide show
  1. package/dist/HierarchicalTrackSelectorWidget/components/faceted/FacetFilter.js +13 -6
  2. package/dist/HierarchicalTrackSelectorWidget/components/tree/TrackLabel.js +22 -47
  3. package/dist/HierarchicalTrackSelectorWidget/generateHierarchy.d.ts +14 -11
  4. package/dist/HierarchicalTrackSelectorWidget/generateHierarchy.js +2 -2
  5. package/dist/HierarchicalTrackSelectorWidget/model.js +9 -2
  6. package/esm/HierarchicalTrackSelectorWidget/components/faceted/FacetFilter.js +13 -6
  7. package/esm/HierarchicalTrackSelectorWidget/components/tree/TrackLabel.js +23 -25
  8. package/esm/HierarchicalTrackSelectorWidget/generateHierarchy.d.ts +14 -11
  9. package/esm/HierarchicalTrackSelectorWidget/generateHierarchy.js +2 -2
  10. package/esm/HierarchicalTrackSelectorWidget/model.js +9 -2
  11. package/package.json +2 -2
package/dist/HierarchicalTrackSelectorWidget/components/faceted/FacetFilter.js CHANGED
@@ -33,6 +33,7 @@ const mui_1 = require("tss-react/mui");
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  const Clear_1 = __importDefault(require("@mui/icons-material/Clear"));
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  const Minimize_1 = __importDefault(require("@mui/icons-material/Minimize"));
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  const Add_1 = __importDefault(require("@mui/icons-material/Add"));
36
+ const util_1 = require("@jbrowse/core/util");
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  const useStyles = (0, mui_1.makeStyles)()(theme => ({
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  facet: {
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  margin: 0,
@@ -42,17 +43,23 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
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  marginBottom: theme.spacing(2),
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  },
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  }));
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+ function ClearButton({ onClick }) {
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+ return (react_1.default.createElement(material_1.Tooltip, { title: "Clear selection on this facet filter" },
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+ react_1.default.createElement(material_1.IconButton, { onClick: () => onClick(), size: "small" },
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+ react_1.default.createElement(Clear_1.default, null))));
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+ }
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+ function ExpandButton({ visible, onClick, }) {
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+ return (react_1.default.createElement(material_1.Tooltip, { title: "Minimize/expand this facet filter" },
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+ react_1.default.createElement(material_1.IconButton, { onClick: () => onClick(), size: "small" }, visible ? react_1.default.createElement(Minimize_1.default, null) : react_1.default.createElement(Add_1.default, null))));
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+ }
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  function FacetFilter({ column, vals, width, dispatch, filters, }) {
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  const { classes } = useStyles();
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  const [visible, setVisible] = (0, react_1.useState)(true);
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  return (react_1.default.createElement(material_1.FormControl, { key: column.field, className: classes.facet, style: { width } },
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  react_1.default.createElement("div", { style: { display: 'flex' } },
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  react_1.default.createElement(material_1.Typography, null, column.field),
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- react_1.default.createElement(material_1.Tooltip, { title: "Clear selection on this facet filter" },
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- react_1.default.createElement(material_1.IconButton, { onClick: () => dispatch({ key: column.field, val: [] }), size: "small" },
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- react_1.default.createElement(Clear_1.default, null))),
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- react_1.default.createElement(material_1.Tooltip, { title: "Minimize/expand this facet filter" },
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- react_1.default.createElement(material_1.IconButton, { onClick: () => setVisible(!visible), size: "small" }, visible ? react_1.default.createElement(Minimize_1.default, null) : react_1.default.createElement(Add_1.default, null)))),
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+ react_1.default.createElement(ClearButton, { onClick: () => dispatch({ key: column.field, val: [] }) }),
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+ react_1.default.createElement(ExpandButton, { visible: visible, onClick: () => setVisible(!visible) })),
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  visible ? (react_1.default.createElement(material_1.Select, { multiple: true, native: true, className: classes.select, value: filters[column.field], onChange: event => {
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  dispatch({
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  key: column.field,
@@ -64,7 +71,7 @@ function FacetFilter({ column, vals, width, dispatch, filters, }) {
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  } }, vals
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  .sort((a, b) => a[0].localeCompare(b[0]))
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  .map(([name, count]) => (react_1.default.createElement("option", { key: name, value: name },
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- name,
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+ (0, util_1.coarseStripHTML)(name),
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  " (",
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  count,
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  ")"))))) : null));
package/dist/HierarchicalTrackSelectorWidget/components/tree/TrackLabel.js CHANGED
@@ -1,35 +1,11 @@
1
1
  "use strict";
2
- var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
3
- if (k2 === undefined) k2 = k;
4
- var desc = Object.getOwnPropertyDescriptor(m, k);
5
- if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
6
- desc = { enumerable: true, get: function() { return m[k]; } };
7
- }
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- Object.defineProperty(o, k2, desc);
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- }) : (function(o, m, k, k2) {
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- if (k2 === undefined) k2 = k;
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- o[k2] = m[k];
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- }));
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- var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
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- Object.defineProperty(o, "default", { enumerable: true, value: v });
15
- }) : function(o, v) {
16
- o["default"] = v;
17
- });
18
- var __importStar = (this && this.__importStar) || function (mod) {
19
- if (mod && mod.__esModule) return mod;
20
- var result = {};
21
- if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
22
- __setModuleDefault(result, mod);
23
- return result;
24
- };
25
2
  var __importDefault = (this && this.__importDefault) || function (mod) {
26
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  return (mod && mod.__esModule) ? mod : { "default": mod };
27
4
  };
28
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  Object.defineProperty(exports, "__esModule", { value: true });
29
- const react_1 = __importStar(require("react"));
6
+ const react_1 = __importDefault(require("react"));
30
7
  const material_1 = require("@mui/material");
31
8
  const mui_1 = require("tss-react/mui");
32
- const Menu_1 = __importDefault(require("@jbrowse/core/ui/Menu"));
33
9
  const util_1 = require("@jbrowse/core/util");
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10
  const SanitizedHTML_1 = __importDefault(require("@jbrowse/core/ui/SanitizedHTML"));
35
11
  const configuration_1 = require("@jbrowse/core/configuration");
@@ -37,6 +13,7 @@ const configuration_1 = require("@jbrowse/core/configuration");
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13
  const MoreHoriz_1 = __importDefault(require("@mui/icons-material/MoreHoriz"));
38
14
  // locals
39
15
  const util_2 = require("../util");
16
+ const CascadingMenuButton_1 = __importDefault(require("@jbrowse/core/ui/CascadingMenuButton"));
40
17
  const useStyles = (0, mui_1.makeStyles)()(theme => ({
41
18
  compactCheckbox: {
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  padding: 0,
@@ -49,10 +26,8 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
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26
  },
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  }));
51
28
  function TrackLabel({ data }) {
52
- var _a, _b;
53
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  const { classes } = useStyles();
54
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  const { checked, conf, model, drawerPosition, id, name, onChange, selected } = data;
55
- const [info, setInfo] = (0, react_1.useState)();
56
31
  const description = (conf && (0, configuration_1.readConfObject)(conf, ['description'])) || '';
57
32
  return (react_1.default.createElement(react_1.default.Fragment, null,
58
33
  react_1.default.createElement(material_1.Tooltip, { title: description + (selected ? ' (in selection)' : ''), placement: drawerPosition === 'left' ? 'right' : 'left' },
@@ -61,25 +36,25 @@ function TrackLabel({ data }) {
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  'data-testid': `htsTrackEntry-${id}`,
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  } }), label: react_1.default.createElement("div", { "data-testid": `htsTrackLabel-${id}`, style: { background: selected ? '#cccc' : undefined } },
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  react_1.default.createElement(SanitizedHTML_1.default, { html: name })) })),
64
- react_1.default.createElement(material_1.IconButton, { onClick: e => setInfo({ target: e.currentTarget, id, conf }), style: { padding: 0 }, "data-testid": `htsTrackEntryMenu-${id}` },
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- react_1.default.createElement(MoreHoriz_1.default, null)),
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- info ? (react_1.default.createElement(Menu_1.default, { anchorEl: info === null || info === void 0 ? void 0 : info.target, menuItems: [
67
- ...(((_b = (_a = (0, util_1.getSession)(model)).getTrackActionMenuItems) === null || _b === void 0 ? void 0 : _b.call(_a, info.conf)) || []),
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- {
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- label: 'Add to selection',
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- onClick: () => model.addToSelection([info.conf]),
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- },
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- ...(selected
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- ? [
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- {
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- label: 'Remove from selection',
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- onClick: () => model.removeFromSelection([info.conf]),
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- },
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- ]
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- : []),
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- ], onMenuItemClick: (_event, callback) => {
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- callback();
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- setInfo(undefined);
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- }, open: Boolean(info), onClose: () => setInfo(undefined) })) : null));
39
+ react_1.default.createElement(TrackMenuButton, { model: model, selected: selected, id: id, conf: conf })));
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40
  }
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  exports.default = TrackLabel;
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+ function TrackMenuButton({ id, model, selected, conf, }) {
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+ var _a, _b;
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+ return (react_1.default.createElement(CascadingMenuButton_1.default, { style: { padding: 0 }, "data-testid": `htsTrackEntryMenu-${id}`, menuItems: [
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+ ...(((_b = (_a = (0, util_1.getSession)(model)).getTrackActionMenuItems) === null || _b === void 0 ? void 0 : _b.call(_a, conf)) || []),
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+ {
47
+ label: 'Add to selection',
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+ onClick: () => model.addToSelection([conf]),
49
+ },
50
+ ...(selected
51
+ ? [
52
+ {
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+ label: 'Remove from selection',
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+ onClick: () => model.removeFromSelection([conf]),
55
+ },
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+ ]
57
+ : []),
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+ ] },
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+ react_1.default.createElement(MoreHoriz_1.default, null)));
60
+ }
package/dist/HierarchicalTrackSelectorWidget/generateHierarchy.d.ts CHANGED
@@ -7,15 +7,18 @@ export interface TreeNode {
7
7
  isOpenByDefault?: boolean;
8
8
  children: TreeNode[];
9
9
  }
10
- export declare function generateHierarchy(model: {
11
- filterText: string;
12
- activeSortTrackNames: boolean;
13
- activeSortCategories: boolean;
14
- view?: {
15
- tracks: {
16
- configuration: AnyConfigurationModel;
17
- }[];
10
+ export declare function generateHierarchy({ model, trackConfs, extra, }: {
11
+ model: {
12
+ filterText: string;
13
+ activeSortTrackNames: boolean;
14
+ activeSortCategories: boolean;
15
+ collapsed: Map<string, boolean>;
16
+ view?: {
17
+ tracks: {
18
+ configuration: AnyConfigurationModel;
19
+ }[];
20
+ };
18
21
  };
19
- }, trackConfs: AnyConfigurationModel[], collapsed: {
20
- get: (arg: string) => boolean | undefined;
21
- }, extra?: string): TreeNode[];
22
+ trackConfs: AnyConfigurationModel[];
23
+ extra?: string;
24
+ }): TreeNode[];
package/dist/HierarchicalTrackSelectorWidget/generateHierarchy.js CHANGED
@@ -40,9 +40,9 @@ function sortConfs(confs, sortNames, sortCategories) {
40
40
  }
41
41
  return ret.map(a => a[0]);
42
42
  }
43
- function generateHierarchy(model, trackConfs, collapsed, extra) {
43
+ function generateHierarchy({ model, trackConfs, extra, }) {
44
44
  const hierarchy = { children: [] };
45
- const { filterText, activeSortTrackNames, activeSortCategories, view } = model;
45
+ const { collapsed, filterText, activeSortTrackNames, activeSortCategories, view, } = model;
46
46
  if (!view) {
47
47
  return [];
48
48
  }
package/dist/HierarchicalTrackSelectorWidget/model.js CHANGED
@@ -188,7 +188,11 @@ function stateTreeFactory(pluginManager) {
188
188
  * #method
189
189
  */
190
190
  connectionHierarchy(connection) {
191
- return (0, generateHierarchy_1.generateHierarchy)(self, self.connectionTrackConfigurations(connection), self.collapsed, connection.name);
191
+ return (0, generateHierarchy_1.generateHierarchy)({
192
+ model: self,
193
+ trackConfs: self.connectionTrackConfigurations(connection),
194
+ extra: connection.name,
195
+ });
192
196
  },
193
197
  }))
194
198
  .views(self => ({
@@ -218,7 +222,10 @@ function stateTreeFactory(pluginManager) {
218
222
  .map(s => ({
219
223
  name: s.group,
220
224
  id: s.group,
221
- children: (0, generateHierarchy_1.generateHierarchy)(self, s.tracks, self.collapsed),
225
+ children: (0, generateHierarchy_1.generateHierarchy)({
226
+ model: self,
227
+ trackConfs: s.tracks,
228
+ }),
222
229
  }))
223
230
  // always keep the Tracks entry at idx 0
224
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  .filter((f, idx) => idx === 0 || !!f.children.length),
package/esm/HierarchicalTrackSelectorWidget/components/faceted/FacetFilter.js CHANGED
@@ -5,6 +5,7 @@ import { makeStyles } from 'tss-react/mui';
5
5
  import ClearIcon from '@mui/icons-material/Clear';
6
6
  import MinimizeIcon from '@mui/icons-material/Minimize';
7
7
  import AddIcon from '@mui/icons-material/Add';
8
+ import { coarseStripHTML } from '@jbrowse/core/util';
8
9
  const useStyles = makeStyles()(theme => ({
9
10
  facet: {
10
11
  margin: 0,
@@ -14,17 +15,23 @@ const useStyles = makeStyles()(theme => ({
14
15
  marginBottom: theme.spacing(2),
15
16
  },
16
17
  }));
18
+ function ClearButton({ onClick }) {
19
+ return (React.createElement(Tooltip, { title: "Clear selection on this facet filter" },
20
+ React.createElement(IconButton, { onClick: () => onClick(), size: "small" },
21
+ React.createElement(ClearIcon, null))));
22
+ }
23
+ function ExpandButton({ visible, onClick, }) {
24
+ return (React.createElement(Tooltip, { title: "Minimize/expand this facet filter" },
25
+ React.createElement(IconButton, { onClick: () => onClick(), size: "small" }, visible ? React.createElement(MinimizeIcon, null) : React.createElement(AddIcon, null))));
26
+ }
17
27
  export default function FacetFilter({ column, vals, width, dispatch, filters, }) {
18
28
  const { classes } = useStyles();
19
29
  const [visible, setVisible] = useState(true);
20
30
  return (React.createElement(FormControl, { key: column.field, className: classes.facet, style: { width } },
21
31
  React.createElement("div", { style: { display: 'flex' } },
22
32
  React.createElement(Typography, null, column.field),
23
- React.createElement(Tooltip, { title: "Clear selection on this facet filter" },
24
- React.createElement(IconButton, { onClick: () => dispatch({ key: column.field, val: [] }), size: "small" },
25
- React.createElement(ClearIcon, null))),
26
- React.createElement(Tooltip, { title: "Minimize/expand this facet filter" },
27
- React.createElement(IconButton, { onClick: () => setVisible(!visible), size: "small" }, visible ? React.createElement(MinimizeIcon, null) : React.createElement(AddIcon, null)))),
33
+ React.createElement(ClearButton, { onClick: () => dispatch({ key: column.field, val: [] }) }),
34
+ React.createElement(ExpandButton, { visible: visible, onClick: () => setVisible(!visible) })),
28
35
  visible ? (React.createElement(Select, { multiple: true, native: true, className: classes.select, value: filters[column.field], onChange: event => {
29
36
  dispatch({
30
37
  key: column.field,
@@ -36,7 +43,7 @@ export default function FacetFilter({ column, vals, width, dispatch, filters, })
36
43
  } }, vals
37
44
  .sort((a, b) => a[0].localeCompare(b[0]))
38
45
  .map(([name, count]) => (React.createElement("option", { key: name, value: name },
39
- name,
46
+ coarseStripHTML(name),
40
47
  " (",
41
48
  count,
42
49
  ")"))))) : null));
package/esm/HierarchicalTrackSelectorWidget/components/tree/TrackLabel.js CHANGED
@@ -1,7 +1,6 @@
1
- import React, { useState } from 'react';
2
- import { Checkbox, FormControlLabel, IconButton, Tooltip } from '@mui/material';
1
+ import React from 'react';
2
+ import { Checkbox, FormControlLabel, Tooltip } from '@mui/material';
3
3
  import { makeStyles } from 'tss-react/mui';
4
- import JBrowseMenu from '@jbrowse/core/ui/Menu';
5
4
  import { getSession } from '@jbrowse/core/util';
6
5
  import SanitizedHTML from '@jbrowse/core/ui/SanitizedHTML';
7
6
  import { readConfObject, } from '@jbrowse/core/configuration';
@@ -9,6 +8,7 @@ import { readConfObject, } from '@jbrowse/core/configuration';
9
8
  import MoreHorizIcon from '@mui/icons-material/MoreHoriz';
10
9
  // locals
11
10
  import { isUnsupported } from '../util';
11
+ import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
12
12
  const useStyles = makeStyles()(theme => ({
13
13
  compactCheckbox: {
14
14
  padding: 0,
@@ -21,10 +21,8 @@ const useStyles = makeStyles()(theme => ({
21
21
  },
22
22
  }));
23
23
  export default function TrackLabel({ data }) {
24
- var _a, _b;
25
24
  const { classes } = useStyles();
26
25
  const { checked, conf, model, drawerPosition, id, name, onChange, selected } = data;
27
- const [info, setInfo] = useState();
28
26
  const description = (conf && readConfObject(conf, ['description'])) || '';
29
27
  return (React.createElement(React.Fragment, null,
30
28
  React.createElement(Tooltip, { title: description + (selected ? ' (in selection)' : ''), placement: drawerPosition === 'left' ? 'right' : 'left' },
@@ -33,24 +31,24 @@ export default function TrackLabel({ data }) {
33
31
  'data-testid': `htsTrackEntry-${id}`,
34
32
  } }), label: React.createElement("div", { "data-testid": `htsTrackLabel-${id}`, style: { background: selected ? '#cccc' : undefined } },
35
33
  React.createElement(SanitizedHTML, { html: name })) })),
36
- React.createElement(IconButton, { onClick: e => setInfo({ target: e.currentTarget, id, conf }), style: { padding: 0 }, "data-testid": `htsTrackEntryMenu-${id}` },
37
- React.createElement(MoreHorizIcon, null)),
38
- info ? (React.createElement(JBrowseMenu, { anchorEl: info === null || info === void 0 ? void 0 : info.target, menuItems: [
39
- ...(((_b = (_a = getSession(model)).getTrackActionMenuItems) === null || _b === void 0 ? void 0 : _b.call(_a, info.conf)) || []),
40
- {
41
- label: 'Add to selection',
42
- onClick: () => model.addToSelection([info.conf]),
43
- },
44
- ...(selected
45
- ? [
46
- {
47
- label: 'Remove from selection',
48
- onClick: () => model.removeFromSelection([info.conf]),
49
- },
50
- ]
51
- : []),
52
- ], onMenuItemClick: (_event, callback) => {
53
- callback();
54
- setInfo(undefined);
55
- }, open: Boolean(info), onClose: () => setInfo(undefined) })) : null));
34
+ React.createElement(TrackMenuButton, { model: model, selected: selected, id: id, conf: conf })));
35
+ }
36
+ function TrackMenuButton({ id, model, selected, conf, }) {
37
+ var _a, _b;
38
+ return (React.createElement(CascadingMenuButton, { style: { padding: 0 }, "data-testid": `htsTrackEntryMenu-${id}`, menuItems: [
39
+ ...(((_b = (_a = getSession(model)).getTrackActionMenuItems) === null || _b === void 0 ? void 0 : _b.call(_a, conf)) || []),
40
+ {
41
+ label: 'Add to selection',
42
+ onClick: () => model.addToSelection([conf]),
43
+ },
44
+ ...(selected
45
+ ? [
46
+ {
47
+ label: 'Remove from selection',
48
+ onClick: () => model.removeFromSelection([conf]),
49
+ },
50
+ ]
51
+ : []),
52
+ ] },
53
+ React.createElement(MoreHorizIcon, null)));
56
54
  }
package/esm/HierarchicalTrackSelectorWidget/generateHierarchy.d.ts CHANGED
@@ -7,15 +7,18 @@ export interface TreeNode {
7
7
  isOpenByDefault?: boolean;
8
8
  children: TreeNode[];
9
9
  }
10
- export declare function generateHierarchy(model: {
11
- filterText: string;
12
- activeSortTrackNames: boolean;
13
- activeSortCategories: boolean;
14
- view?: {
15
- tracks: {
16
- configuration: AnyConfigurationModel;
17
- }[];
10
+ export declare function generateHierarchy({ model, trackConfs, extra, }: {
11
+ model: {
12
+ filterText: string;
13
+ activeSortTrackNames: boolean;
14
+ activeSortCategories: boolean;
15
+ collapsed: Map<string, boolean>;
16
+ view?: {
17
+ tracks: {
18
+ configuration: AnyConfigurationModel;
19
+ }[];
20
+ };
18
21
  };
19
- }, trackConfs: AnyConfigurationModel[], collapsed: {
20
- get: (arg: string) => boolean | undefined;
21
- }, extra?: string): TreeNode[];
22
+ trackConfs: AnyConfigurationModel[];
23
+ extra?: string;
24
+ }): TreeNode[];
package/esm/HierarchicalTrackSelectorWidget/generateHierarchy.js CHANGED
@@ -37,9 +37,9 @@ function sortConfs(confs, sortNames, sortCategories) {
37
37
  }
38
38
  return ret.map(a => a[0]);
39
39
  }
40
- export function generateHierarchy(model, trackConfs, collapsed, extra) {
40
+ export function generateHierarchy({ model, trackConfs, extra, }) {
41
41
  const hierarchy = { children: [] };
42
- const { filterText, activeSortTrackNames, activeSortCategories, view } = model;
42
+ const { collapsed, filterText, activeSortTrackNames, activeSortCategories, view, } = model;
43
43
  if (!view) {
44
44
  return [];
45
45
  }
package/esm/HierarchicalTrackSelectorWidget/model.js CHANGED
@@ -186,7 +186,11 @@ export default function stateTreeFactory(pluginManager) {
186
186
  * #method
187
187
  */
188
188
  connectionHierarchy(connection) {
189
- return generateHierarchy(self, self.connectionTrackConfigurations(connection), self.collapsed, connection.name);
189
+ return generateHierarchy({
190
+ model: self,
191
+ trackConfs: self.connectionTrackConfigurations(connection),
192
+ extra: connection.name,
193
+ });
190
194
  },
191
195
  }))
192
196
  .views(self => ({
@@ -216,7 +220,10 @@ export default function stateTreeFactory(pluginManager) {
216
220
  .map(s => ({
217
221
  name: s.group,
218
222
  id: s.group,
219
- children: generateHierarchy(self, s.tracks, self.collapsed),
223
+ children: generateHierarchy({
224
+ model: self,
225
+ trackConfs: s.tracks,
226
+ }),
220
227
  }))
221
228
  // always keep the Tracks entry at idx 0
222
229
  .filter((f, idx) => idx === 0 || !!f.children.length),
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-data-management",
3
- "version": "2.7.0",
3
+ "version": "2.7.1",
4
4
  "description": "JBrowse 2 linear genome view",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -61,5 +61,5 @@
61
61
  "distModule": "esm/index.js",
62
62
  "srcModule": "src/index.ts",
63
63
  "module": "esm/index.js",
64
- "gitHead": "dbe7fb1af01fc89f833d2744635eb44a17365b41"
64
+ "gitHead": "2cda1611eebd12517f2a3cfc1b612face27005d4"
65
65
  }