@jbrowse/plugin-grid-bookmark 2.13.1 → 2.14.0

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Files changed (37) hide show
  1. package/dist/GridBookmarkWidget/components/AssemblySelector.js +4 -2
  2. package/dist/GridBookmarkWidget/components/BookmarkGrid.js +3 -1
  3. package/dist/GridBookmarkWidget/components/GridBookmarkWidget.d.ts +1 -1
  4. package/dist/GridBookmarkWidget/components/GridBookmarkWidget.js +0 -3
  5. package/dist/GridBookmarkWidget/components/Highlight/Highlight.js +5 -3
  6. package/dist/GridBookmarkWidget/components/Highlight/OverviewHighlight.js +1 -1
  7. package/dist/GridBookmarkWidget/components/Highlight/index.js +6 -6
  8. package/dist/GridBookmarkWidget/components/dialogs/DeleteBookmarksDialog.js +3 -1
  9. package/dist/GridBookmarkWidget/components/dialogs/EditBookmarkLabelDialog.js +4 -2
  10. package/dist/GridBookmarkWidget/components/dialogs/EditHighlightColorDialog.js +6 -2
  11. package/dist/GridBookmarkWidget/components/dialogs/ExportBookmarksDialog.js +3 -1
  12. package/dist/GridBookmarkWidget/components/dialogs/HighlightSettingsDialog.js +3 -1
  13. package/dist/GridBookmarkWidget/components/dialogs/ImportBookmarksDialog.js +22 -17
  14. package/dist/GridBookmarkWidget/components/dialogs/ShareBookmarksDialog.js +8 -12
  15. package/dist/GridBookmarkWidget/model.d.ts +2 -2
  16. package/dist/GridBookmarkWidget/model.js +5 -1
  17. package/dist/GridBookmarkWidget/utils.js +6 -3
  18. package/dist/index.js +23 -8
  19. package/esm/GridBookmarkWidget/components/AssemblySelector.js +4 -2
  20. package/esm/GridBookmarkWidget/components/BookmarkGrid.js +3 -1
  21. package/esm/GridBookmarkWidget/components/GridBookmarkWidget.d.ts +1 -1
  22. package/esm/GridBookmarkWidget/components/GridBookmarkWidget.js +0 -3
  23. package/esm/GridBookmarkWidget/components/Highlight/Highlight.js +5 -3
  24. package/esm/GridBookmarkWidget/components/Highlight/OverviewHighlight.js +1 -1
  25. package/esm/GridBookmarkWidget/components/Highlight/index.js +6 -6
  26. package/esm/GridBookmarkWidget/components/dialogs/DeleteBookmarksDialog.js +3 -1
  27. package/esm/GridBookmarkWidget/components/dialogs/EditBookmarkLabelDialog.js +4 -2
  28. package/esm/GridBookmarkWidget/components/dialogs/EditHighlightColorDialog.js +6 -2
  29. package/esm/GridBookmarkWidget/components/dialogs/ExportBookmarksDialog.js +3 -1
  30. package/esm/GridBookmarkWidget/components/dialogs/HighlightSettingsDialog.js +3 -1
  31. package/esm/GridBookmarkWidget/components/dialogs/ImportBookmarksDialog.js +22 -17
  32. package/esm/GridBookmarkWidget/components/dialogs/ShareBookmarksDialog.js +8 -12
  33. package/esm/GridBookmarkWidget/model.d.ts +2 -2
  34. package/esm/GridBookmarkWidget/model.js +5 -1
  35. package/esm/GridBookmarkWidget/utils.js +6 -3
  36. package/esm/index.js +23 -8
  37. package/package.json +3 -3
package/dist/GridBookmarkWidget/components/AssemblySelector.js CHANGED
@@ -8,14 +8,16 @@ const mobx_react_1 = require("mobx-react");
8
8
  const material_1 = require("@mui/material");
9
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  const AssemblySelector = (0, mobx_react_1.observer)(function ({ model, }) {
10
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  const { validAssemblies, selectedAssemblies } = model;
11
- const noAssemblies = validAssemblies.size === 0 ? true : false;
11
+ const noAssemblies = validAssemblies.size === 0;
12
12
  const label = 'Select assemblies';
13
13
  const id = 'select-assemblies-label';
14
14
  const selectedSet = new Set(selectedAssemblies);
15
15
  const isAllSelected = [...validAssemblies].every(e => selectedSet.has(e));
16
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  return (react_1.default.createElement(material_1.FormControl, { disabled: noAssemblies, fullWidth: true },
17
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  react_1.default.createElement(material_1.InputLabel, { id: id }, label),
18
- react_1.default.createElement(material_1.Select, { labelId: id, multiple: true, value: selectedAssemblies, onChange: event => model.setSelectedAssemblies([...event.target.value]), input: react_1.default.createElement(material_1.OutlinedInput, { label: label }), renderValue: selected => selected.join(', ') },
18
+ react_1.default.createElement(material_1.Select, { labelId: id, multiple: true, value: selectedAssemblies, onChange: event => {
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+ model.setSelectedAssemblies([...event.target.value]);
20
+ }, input: react_1.default.createElement(material_1.OutlinedInput, { label: label }), renderValue: selected => selected.join(', ') },
19
21
  react_1.default.createElement(material_1.MenuItem, { onClickCapture: event => {
20
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  // onClickCapture allows us to avoid the parent Select onChange from triggering
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  if (isAllSelected) {
package/dist/GridBookmarkWidget/components/BookmarkGrid.js CHANGED
@@ -110,7 +110,9 @@ const BookmarkGrid = (0, mobx_react_1.observer)(function ({ model, }) {
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  const target = rows[row.id];
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  model.updateBookmarkLabel(target, row.label);
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  return row;
113
- }, onProcessRowUpdateError: e => session.notifyError(`${e}`, e), checkboxSelection: true, onRowSelectionModelChange: newRowSelectionModel => {
113
+ }, onProcessRowUpdateError: e => {
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+ session.notifyError(`${e}`, e);
115
+ }, checkboxSelection: true, onRowSelectionModelChange: newRowSelectionModel => {
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  if (bookmarksWithValidAssemblies.length > 0) {
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  model.setSelectedBookmarks(newRowSelectionModel.map(value => ({
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  ...rows[value],
package/dist/GridBookmarkWidget/components/GridBookmarkWidget.d.ts CHANGED
@@ -2,5 +2,5 @@ import React from 'react';
2
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  import { GridBookmarkModel } from '../model';
3
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  declare const GridBookmarkWidget: ({ model, }: {
4
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  model: GridBookmarkModel;
5
- }) => React.JSX.Element | null;
5
+ }) => React.JSX.Element;
6
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  export default GridBookmarkWidget;
package/dist/GridBookmarkWidget/components/GridBookmarkWidget.js CHANGED
@@ -57,9 +57,6 @@ const useStyles = (0, mui_1.makeStyles)()({
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  });
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  const GridBookmarkWidget = (0, mobx_react_1.observer)(function GridBookmarkWidget({ model, }) {
59
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  const { classes } = useStyles();
60
- if (!model) {
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- return null;
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- }
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  return (react_1.default.createElement("div", null,
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  react_1.default.createElement(material_1.Alert, { severity: "info" },
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  "Click and type within the ",
package/dist/GridBookmarkWidget/components/Highlight/Highlight.js CHANGED
@@ -72,15 +72,17 @@ const Highlight = (0, mobx_react_1.observer)(function Highlight({ model }) {
72
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  : undefined;
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  })
74
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  .filter(util_1.notEmpty)
75
- .map(({ left, width, highlight, label }, idx) => (react_1.default.createElement("div", { key: `${left}_${width}_${idx}`, className: classes.highlight, style: {
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+ .map(({ left, width, highlight, label }, idx) => (react_1.default.createElement("div", {
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+ /* biome-ignore lint/suspicious/noArrayIndexKey: */
77
+ key: `${left}_${width}_${idx}`, className: classes.highlight, style: {
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  left,
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  width,
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  background: highlight,
79
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  } }, showBookmarkLabels ? (react_1.default.createElement(material_1.Tooltip, { title: label, arrow: true },
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  react_1.default.createElement(Bookmark_1.default, { fontSize: "small", sx: {
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- color: `${(0, colord_1.colord)(highlight).alpha() !== 0
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+ color: (0, colord_1.colord)(highlight).alpha() !== 0
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  ? (0, colord_1.colord)(highlight).alpha(0.8).toRgbString()
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- : (0, colord_1.colord)(highlight).alpha(0).toRgbString()}`,
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+ : (0, colord_1.colord)(highlight).alpha(0).toRgbString(),
84
86
  } }))) : null)))
85
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  : null;
86
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  });
package/dist/GridBookmarkWidget/components/Highlight/OverviewHighlight.js CHANGED
@@ -69,7 +69,7 @@ const OverviewHighlight = (0, mobx_react_1.observer)(function OverviewHighlight(
69
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  .filter(util_1.notEmpty)
70
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  .map((obj, idx) => {
71
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  const { left, width, highlight, label } = obj;
72
- return (react_1.default.createElement(material_1.Tooltip, { key: JSON.stringify(obj) + '-' + idx, title: showBookmarkLabels ? label : '', arrow: true },
72
+ return (react_1.default.createElement(material_1.Tooltip, { key: `${JSON.stringify(obj)}-${idx}`, title: showBookmarkLabels ? label : '', arrow: true },
73
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  react_1.default.createElement("div", { className: classes.highlight, style: {
74
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  left,
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  width,
package/dist/GridBookmarkWidget/components/Highlight/index.js CHANGED
@@ -11,18 +11,18 @@ const OverviewHighlight_1 = __importDefault(require("./OverviewHighlight"));
11
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  function AddHighlightModelF(pluginManager) {
12
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  pluginManager.addToExtensionPoint('LinearGenomeView-TracksContainerComponent',
13
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  // @ts-expect-error
14
- (rest = [], { model }) => {
14
+ (rest, { model }) => {
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  return [
16
- ...rest,
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- react_1.default.createElement(Highlight_1.default, { key: `highlight_grid_bookmark`, model: model }),
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+ ...(rest || []),
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+ react_1.default.createElement(Highlight_1.default, { key: "highlight_grid_bookmark", model: model }),
18
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  ];
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  });
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  pluginManager.addToExtensionPoint('LinearGenomeView-OverviewScalebarComponent',
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  // @ts-expect-error
22
- (rest = [], { model, overview }) => {
22
+ (rest, { model, overview }) => {
23
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  return [
24
- ...rest,
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- react_1.default.createElement(OverviewHighlight_1.default, { key: `overview_highlight_grid_bookmark`, model: model, overview: overview }),
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+ ...(rest || []),
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+ react_1.default.createElement(OverviewHighlight_1.default, { key: "overview_highlight_grid_bookmark", model: model, overview: overview }),
26
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  ];
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  });
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  }
package/dist/GridBookmarkWidget/components/dialogs/DeleteBookmarksDialog.js CHANGED
@@ -17,7 +17,9 @@ const DeleteBookmarksDialog = (0, mobx_react_1.observer)(function ({ onClose, mo
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  react_1.default.createElement("br", null),
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  react_1.default.createElement("span", null, "Use the checkboxes to select individual bookmarks to delete."))) : ('Only selected bookmarks will be deleted.'))),
19
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  react_1.default.createElement(material_1.DialogActions, null,
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- react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => onClose() }, "Cancel"),
20
+ react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
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+ onClose();
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+ } }, "Cancel"),
21
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  react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", onClick: () => {
22
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  if (deleteAll) {
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  model.clearAllBookmarks();
package/dist/GridBookmarkWidget/components/dialogs/EditBookmarkLabelDialog.js CHANGED
@@ -37,10 +37,12 @@ const EditBookmarkLabelDialog = (0, mobx_react_1.observer)(function ({ model, on
37
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  ' ',
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  react_1.default.createElement("strong", null, (0, util_1.assembleLocString)(dialogRow.correspondingObj)),
39
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  ":"),
40
- react_1.default.createElement(material_1.TextField, { fullWidth: true, inputProps: { 'data-testid': 'edit-bookmark-label-field' }, variant: "outlined", value: newLabel, onChange: e => setNewLabel(e.target.value), autoFocus: true })),
40
+ react_1.default.createElement(material_1.TextField, { fullWidth: true, inputProps: { 'data-testid': 'edit-bookmark-label-field' }, variant: "outlined", value: newLabel, onChange: e => {
41
+ setNewLabel(e.target.value);
42
+ }, autoFocus: true })),
41
43
  react_1.default.createElement(material_1.DialogActions, null,
42
44
  react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", onClick: () => {
43
- if (newLabel && dialogRow) {
45
+ if (newLabel) {
44
46
  model.updateBookmarkLabel(dialogRow, newLabel);
45
47
  }
46
48
  setNewLabel('');
package/dist/GridBookmarkWidget/components/dialogs/EditHighlightColorDialog.js CHANGED
@@ -37,9 +37,13 @@ const EditHighlightColorDialog = (0, mobx_react_1.observer)(function ({ onClose,
37
37
  react_1.default.createElement(material_1.DialogContent, null,
38
38
  react_1.default.createElement(material_1.Typography, { variant: "h6" }, "Bulk highlight selector"),
39
39
  react_1.default.createElement(material_1.Alert, { severity: "info" }, editNone ? (react_1.default.createElement("span", null, "Use the checkboxes to select individual bookmarks to edit.")) : ('Only selected bookmarks will be edited.')),
40
- !editNone ? (react_1.default.createElement(ColorPicker_1.ColorPicker, { color: color, onChange: event => setColor(event) })) : null),
40
+ !editNone ? (react_1.default.createElement(ColorPicker_1.ColorPicker, { color: color, onChange: event => {
41
+ setColor(event);
42
+ } })) : null),
41
43
  react_1.default.createElement(material_1.DialogActions, null,
42
- react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => onClose() }, "Cancel"),
44
+ react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
45
+ onClose();
46
+ } }, "Cancel"),
43
47
  react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", onClick: () => {
44
48
  model.updateBulkBookmarkHighlights(color);
45
49
  onClose();
package/dist/GridBookmarkWidget/components/dialogs/ExportBookmarksDialog.js CHANGED
@@ -59,7 +59,9 @@ const ExportBookmarksDialog = (0, mobx_react_1.observer)(function ExportBookmark
59
59
  react_1.default.createElement("span", null, "Use the checkboxes to select individual bookmarks to export."))) : ('Only selected bookmarks will be exported.')),
60
60
  react_1.default.createElement("div", { className: classes.flexItem },
61
61
  react_1.default.createElement(material_1.Typography, null, "Format to download:"),
62
- react_1.default.createElement(material_1.Select, { size: "small", value: fileType, onChange: event => setFileType(event.target.value) },
62
+ react_1.default.createElement(material_1.Select, { size: "small", value: fileType, onChange: event => {
63
+ setFileType(event.target.value);
64
+ } },
63
65
  react_1.default.createElement(material_1.MenuItem, { value: "BED" }, "BED"),
64
66
  react_1.default.createElement(material_1.MenuItem, { value: "TSV" }, "TSV")))),
65
67
  react_1.default.createElement(material_1.DialogActions, null,
package/dist/GridBookmarkWidget/components/dialogs/HighlightSettingsDialog.js CHANGED
@@ -22,6 +22,8 @@ const HighlightSettingsDialog = (0, mobx_react_1.observer)(function ({ onClose,
22
22
  } }),
23
23
  react_1.default.createElement(material_1.Typography, null, "Toggle 'bookmark' icon on LGV tracks"))),
24
24
  react_1.default.createElement(material_1.DialogActions, null,
25
- react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", onClick: () => onClose() }, "Close"))));
25
+ react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", onClick: () => {
26
+ onClose();
27
+ } }, "Close"))));
26
28
  });
27
29
  exports.default = HighlightSettingsDialog;
package/dist/GridBookmarkWidget/components/dialogs/ImportBookmarksDialog.js CHANGED
@@ -40,17 +40,14 @@ const Publish_1 = __importDefault(require("@mui/icons-material/Publish"));
40
40
  const ExpandMore_1 = __importDefault(require("@mui/icons-material/ExpandMore"));
41
41
  const utils_1 = require("../../utils");
42
42
  const sessionSharing_1 = require("../../sessionSharing");
43
- const useStyles = (0, mui_1.makeStyles)()(theme => {
44
- var _a;
45
- return ({
46
- expandIcon: {
47
- color: ((_a = theme.palette.tertiary) === null || _a === void 0 ? void 0 : _a.contrastText) || '#fff',
48
- },
49
- minWidth: {
50
- minWidth: 500,
51
- },
52
- });
53
- });
43
+ const useStyles = (0, mui_1.makeStyles)()(theme => ({
44
+ expandIcon: {
45
+ color: theme.palette.tertiary.contrastText || '#fff',
46
+ },
47
+ minWidth: {
48
+ minWidth: 500,
49
+ },
50
+ }));
54
51
  async function getBookmarksFromShareLink(shareLink, shareURL) {
55
52
  const defaultURL = 'https://share.jbrowse.org/api/v1/';
56
53
  const urlParams = new URL(shareLink);
@@ -75,7 +72,7 @@ async function getBookmarksFromTSVFile(lines) {
75
72
  const [refName, start, end, label, assemblyName] = line.split('\t');
76
73
  return {
77
74
  assemblyName: assemblyName,
78
- refName,
75
+ refName: refName,
79
76
  start: +start,
80
77
  end: +end,
81
78
  label: label === '.' ? undefined : label,
@@ -89,7 +86,7 @@ async function getBookmarksFromBEDFile(lines, selectedAsm) {
89
86
  const [refName, start, end, label] = line.split('\t');
90
87
  return {
91
88
  assemblyName: selectedAsm,
92
- refName,
89
+ refName: refName,
93
90
  start: +start,
94
91
  end: +end,
95
92
  label: label === '.' ? undefined : label,
@@ -107,18 +104,26 @@ const ImportBookmarksDialog = (0, mobx_react_1.observer)(function ({ onClose, mo
107
104
  const [expanded, setExpanded] = (0, react_1.useState)('shareLinkAccordion');
108
105
  return (react_1.default.createElement(ui_2.Dialog, { open: true, onClose: onClose, maxWidth: "xl", title: "Import bookmarks" },
109
106
  react_1.default.createElement(material_1.DialogContent, { className: classes.minWidth },
110
- react_1.default.createElement(material_1.Accordion, { expanded: expanded === 'shareLinkAccordion', onChange: () => setExpanded('shareLinkAccordion') },
107
+ react_1.default.createElement(material_1.Accordion, { expanded: expanded === 'shareLinkAccordion', onChange: () => {
108
+ setExpanded('shareLinkAccordion');
109
+ } },
111
110
  react_1.default.createElement(material_1.AccordionSummary, { expandIcon: react_1.default.createElement(ExpandMore_1.default, { className: classes.expandIcon }) },
112
111
  react_1.default.createElement(material_1.Typography, { style: { display: 'flex', alignItems: 'center', gap: '5px' } }, "Import from share link")),
113
112
  react_1.default.createElement(material_1.AccordionDetails, null,
114
113
  react_1.default.createElement(material_1.Typography, null, "Paste a bookmark share link generated by the 'Share' button from the bookmarks widget"),
115
- react_1.default.createElement(material_1.TextField, { label: "Enter Share URL", variant: "outlined", fullWidth: true, value: shareLink, onChange: e => setShareLink(e.target.value) }))),
116
- react_1.default.createElement(material_1.Accordion, { expanded: expanded === 'fileAccordion', onChange: () => setExpanded('fileAccordion') },
114
+ react_1.default.createElement(material_1.TextField, { label: "Enter Share URL", variant: "outlined", fullWidth: true, value: shareLink, onChange: e => {
115
+ setShareLink(e.target.value);
116
+ } }))),
117
+ react_1.default.createElement(material_1.Accordion, { expanded: expanded === 'fileAccordion', onChange: () => {
118
+ setExpanded('fileAccordion');
119
+ } },
117
120
  react_1.default.createElement(material_1.AccordionSummary, { expandIcon: react_1.default.createElement(ExpandMore_1.default, { className: classes.expandIcon }) },
118
121
  react_1.default.createElement(material_1.Typography, null, "Import from file")),
119
122
  react_1.default.createElement(material_1.AccordionDetails, null,
120
123
  react_1.default.createElement(ui_1.FileSelector, { location: location, setLocation: setLocation, name: "File", description: `Choose a BED or TSV format file to import. Required TSV column headers are "chrom, start, end, label, assembly_name".` }),
121
- react_1.default.createElement(ui_2.AssemblySelector, { onChange: val => setSelectedAsm(val), helperText: `Select the assembly for BED file.`, session: session, selected: selectedAsm }))),
124
+ react_1.default.createElement(ui_2.AssemblySelector, { onChange: val => {
125
+ setSelectedAsm(val);
126
+ }, helperText: 'Select the assembly for BED file.', session: session, selected: selectedAsm }))),
122
127
  error ? react_1.default.createElement(ui_1.ErrorMessage, { error: error }) : null),
123
128
  react_1.default.createElement(material_1.DialogActions, null,
124
129
  react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: onClose }, "Cancel"),
package/dist/GridBookmarkWidget/components/dialogs/ShareBookmarksDialog.js CHANGED
@@ -54,7 +54,8 @@ const ShareBookmarksDialog = (0, mobx_react_1.observer)(function ({ onClose, mod
54
54
  ? model.allBookmarksModel
55
55
  : model.sharedBookmarksModel;
56
56
  (0, react_1.useEffect)(() => {
57
- let cancelled = false;
57
+ // eslint-disable-next-line @typescript-eslint/no-floating-promises
58
+ ;
58
59
  (async () => {
59
60
  try {
60
61
  if (!(0, util_1.isSessionWithShareURL)(session)) {
@@ -64,14 +65,12 @@ const ShareBookmarksDialog = (0, mobx_react_1.observer)(function ({ onClose, mod
64
65
  const snap = (0, mobx_state_tree_1.getSnapshot)(bookmarksToShare);
65
66
  const locationUrl = new URL(window.location.href);
66
67
  const result = await (0, sessionSharing_1.shareSessionToDynamo)(snap, session.shareURL, locationUrl.href);
67
- if (!cancelled) {
68
- const params = new URLSearchParams(locationUrl.search);
69
- params.set('bookmarks', `share-${result.json.sessionId}`);
70
- params.set('password', result.password);
71
- locationUrl.search = params.toString();
72
- setUrl(locationUrl.href);
73
- setLoading(false);
74
- }
68
+ const params = new URLSearchParams(locationUrl.search);
69
+ params.set('bookmarks', `share-${result.json.sessionId}`);
70
+ params.set('password', result.password);
71
+ locationUrl.search = params.toString();
72
+ setUrl(locationUrl.href);
73
+ setLoading(false);
75
74
  }
76
75
  catch (e) {
77
76
  setError(e);
@@ -80,9 +79,6 @@ const ShareBookmarksDialog = (0, mobx_react_1.observer)(function ({ onClose, mod
80
79
  setLoading(false);
81
80
  }
82
81
  })();
83
- return () => {
84
- cancelled = true;
85
- };
86
82
  }, [bookmarksToShare, session]);
87
83
  return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: onClose, title: "Share bookmarks" },
88
84
  react_1.default.createElement(material_1.DialogContent, { style: { display: 'flex', flexFlow: 'column', gap: '5px' } },
package/dist/GridBookmarkWidget/model.d.ts CHANGED
@@ -21,8 +21,8 @@ declare const LabeledRegionModel: import("mobx-state-tree").IModelType<{
21
21
  export interface IExtendedLGV extends LinearGenomeViewModel {
22
22
  showBookmarkHighlights: boolean;
23
23
  showBookmarkLabels: boolean;
24
- toggleShowBookmarkHighlights: (arg: boolean) => {};
25
- toggleShowBookmarkLabels: (arg: boolean) => {};
24
+ toggleShowBookmarkHighlights: (arg: boolean) => void;
25
+ toggleShowBookmarkLabels: (arg: boolean) => void;
26
26
  }
27
27
  export interface ILabeledRegionModel extends SnapshotIn<typeof LabeledRegionModel> {
28
28
  refName: string;
package/dist/GridBookmarkWidget/model.js CHANGED
@@ -161,7 +161,9 @@ function f(_pluginManager) {
161
161
  * #action
162
162
  */
163
163
  updateBulkBookmarkHighlights(color) {
164
- self.selectedBookmarks.forEach(bookmark => this.updateBookmarkHighlight(bookmark, color));
164
+ self.selectedBookmarks.forEach(bookmark => {
165
+ this.updateBookmarkHighlight(bookmark, color);
166
+ });
165
167
  },
166
168
  /**
167
169
  * #action
@@ -182,6 +184,7 @@ function f(_pluginManager) {
182
184
  const { views } = (0, util_1.getSession)(self);
183
185
  views.forEach(view => {
184
186
  var _a;
187
+ // @ts-expect-error
185
188
  (_a = view.toggleShowBookmarkHighlights) === null || _a === void 0 ? void 0 : _a.call(view, toggle);
186
189
  });
187
190
  },
@@ -192,6 +195,7 @@ function f(_pluginManager) {
192
195
  const { views } = (0, util_1.getSession)(self);
193
196
  views.forEach(view => {
194
197
  var _a;
198
+ // @ts-expect-error
195
199
  (_a = view.toggleShowBookmarkLabels) === null || _a === void 0 ? void 0 : _a.call(view, toggle);
196
200
  });
197
201
  },
package/dist/GridBookmarkWidget/utils.js CHANGED
@@ -68,9 +68,12 @@ function downloadBookmarkFile(fileFormat, model) {
68
68
  const { label } = bookmark;
69
69
  const labelVal = label === '' ? '.' : label;
70
70
  const line = `${bookmark.refName}\t${bookmark.start}\t${bookmark.end}\t${labelVal}\n`;
71
- fileContents[bookmark.assemblyName]
72
- ? fileContents[bookmark.assemblyName].push(line)
73
- : (fileContents[bookmark.assemblyName] = [line]);
71
+ if (fileContents[bookmark.assemblyName]) {
72
+ fileContents[bookmark.assemblyName].push(line);
73
+ }
74
+ else {
75
+ fileContents[bookmark.assemblyName] = [line];
76
+ }
74
77
  });
75
78
  for (const assembly in fileContents) {
76
79
  const fileContent = fileContents[assembly].reduce((a, b) => a + b, fileHeader);
package/dist/index.js CHANGED
@@ -67,9 +67,8 @@ class GridBookmarkPlugin extends Plugin_1.default {
67
67
  navigateNewestBookmark() {
68
68
  const session = (0, util_1.getSession)(self);
69
69
  const bookmarkWidget = self.activateBookmarkWidget();
70
- const regions = bookmarkWidget.bookmarks;
71
- if (regions === null || regions === void 0 ? void 0 : regions.length) {
72
- self.navTo(regions.at(-1));
70
+ if (bookmarkWidget.bookmarks.length) {
71
+ self.navTo(bookmarkWidget.bookmarks.at(-1));
73
72
  }
74
73
  else {
75
74
  session.notify('There are no recent bookmarks to navigate to.', 'info');
@@ -79,7 +78,12 @@ class GridBookmarkPlugin extends Plugin_1.default {
79
78
  if (self.id === (0, util_1.getSession)(self).focusedViewId) {
80
79
  const selectedRegions = self.getSelectedRegions(undefined, undefined);
81
80
  const bookmarkWidget = self.activateBookmarkWidget();
82
- bookmarkWidget.addBookmark(selectedRegions[0]);
81
+ if (!selectedRegions.length) {
82
+ throw new Error('no region selected');
83
+ }
84
+ else {
85
+ bookmarkWidget.addBookmark(selectedRegions[0]);
86
+ }
83
87
  }
84
88
  },
85
89
  }))
@@ -103,21 +107,27 @@ class GridBookmarkPlugin extends Plugin_1.default {
103
107
  {
104
108
  label: 'Bookmark current region',
105
109
  icon: Bookmark_1.default,
106
- onClick: () => self.bookmarkCurrentRegion(),
110
+ onClick: () => {
111
+ self.bookmarkCurrentRegion();
112
+ },
107
113
  },
108
114
  {
109
115
  label: 'Toggle bookmark highlights',
110
116
  icon: Highlight_1.default,
111
117
  type: 'checkbox',
112
118
  checked: self.showBookmarkHighlights,
113
- onClick: () => self.toggleShowBookmarkHighlights(),
119
+ onClick: () => {
120
+ self.toggleShowBookmarkHighlights();
121
+ },
114
122
  },
115
123
  {
116
124
  label: 'Toggle bookmark labels',
117
125
  icon: Label_1.default,
118
126
  type: 'checkbox',
119
127
  checked: self.showBookmarkLabels,
120
- onClick: () => self.toggleShowBookmarkLabels(),
128
+ onClick: () => {
129
+ self.toggleShowBookmarkLabels();
130
+ },
121
131
  },
122
132
  ],
123
133
  },
@@ -133,7 +143,12 @@ class GridBookmarkPlugin extends Plugin_1.default {
133
143
  const { leftOffset, rightOffset } = self;
134
144
  const selectedRegions = self.getSelectedRegions(leftOffset, rightOffset);
135
145
  const bookmarkWidget = self.activateBookmarkWidget();
136
- bookmarkWidget.addBookmark(selectedRegions[0]);
146
+ if (!selectedRegions.length) {
147
+ throw new Error('no regions selected');
148
+ }
149
+ else {
150
+ bookmarkWidget.addBookmark(selectedRegions[0]);
151
+ }
137
152
  },
138
153
  },
139
154
  ];
package/esm/GridBookmarkWidget/components/AssemblySelector.js CHANGED
@@ -3,14 +3,16 @@ import { observer } from 'mobx-react';
3
3
  import { Checkbox, FormControl, InputLabel, ListItemText, MenuItem, OutlinedInput, Select, } from '@mui/material';
4
4
  const AssemblySelector = observer(function ({ model, }) {
5
5
  const { validAssemblies, selectedAssemblies } = model;
6
- const noAssemblies = validAssemblies.size === 0 ? true : false;
6
+ const noAssemblies = validAssemblies.size === 0;
7
7
  const label = 'Select assemblies';
8
8
  const id = 'select-assemblies-label';
9
9
  const selectedSet = new Set(selectedAssemblies);
10
10
  const isAllSelected = [...validAssemblies].every(e => selectedSet.has(e));
11
11
  return (React.createElement(FormControl, { disabled: noAssemblies, fullWidth: true },
12
12
  React.createElement(InputLabel, { id: id }, label),
13
- React.createElement(Select, { labelId: id, multiple: true, value: selectedAssemblies, onChange: event => model.setSelectedAssemblies([...event.target.value]), input: React.createElement(OutlinedInput, { label: label }), renderValue: selected => selected.join(', ') },
13
+ React.createElement(Select, { labelId: id, multiple: true, value: selectedAssemblies, onChange: event => {
14
+ model.setSelectedAssemblies([...event.target.value]);
15
+ }, input: React.createElement(OutlinedInput, { label: label }), renderValue: selected => selected.join(', ') },
14
16
  React.createElement(MenuItem, { onClickCapture: event => {
15
17
  // onClickCapture allows us to avoid the parent Select onChange from triggering
16
18
  if (isAllSelected) {
package/esm/GridBookmarkWidget/components/BookmarkGrid.js CHANGED
@@ -82,7 +82,9 @@ const BookmarkGrid = observer(function ({ model, }) {
82
82
  const target = rows[row.id];
83
83
  model.updateBookmarkLabel(target, row.label);
84
84
  return row;
85
- }, onProcessRowUpdateError: e => session.notifyError(`${e}`, e), checkboxSelection: true, onRowSelectionModelChange: newRowSelectionModel => {
85
+ }, onProcessRowUpdateError: e => {
86
+ session.notifyError(`${e}`, e);
87
+ }, checkboxSelection: true, onRowSelectionModelChange: newRowSelectionModel => {
86
88
  if (bookmarksWithValidAssemblies.length > 0) {
87
89
  model.setSelectedBookmarks(newRowSelectionModel.map(value => ({
88
90
  ...rows[value],
package/esm/GridBookmarkWidget/components/GridBookmarkWidget.d.ts CHANGED
@@ -2,5 +2,5 @@ import React from 'react';
2
2
  import { GridBookmarkModel } from '../model';
3
3
  declare const GridBookmarkWidget: ({ model, }: {
4
4
  model: GridBookmarkModel;
5
- }) => React.JSX.Element | null;
5
+ }) => React.JSX.Element;
6
6
  export default GridBookmarkWidget;
package/esm/GridBookmarkWidget/components/GridBookmarkWidget.js CHANGED
@@ -29,9 +29,6 @@ const useStyles = makeStyles()({
29
29
  });
30
30
  const GridBookmarkWidget = observer(function GridBookmarkWidget({ model, }) {
31
31
  const { classes } = useStyles();
32
- if (!model) {
33
- return null;
34
- }
35
32
  return (React.createElement("div", null,
36
33
  React.createElement(Alert, { severity: "info" },
37
34
  "Click and type within the ",
package/esm/GridBookmarkWidget/components/Highlight/Highlight.js CHANGED
@@ -44,15 +44,17 @@ const Highlight = observer(function Highlight({ model }) {
44
44
  : undefined;
45
45
  })
46
46
  .filter(notEmpty)
47
- .map(({ left, width, highlight, label }, idx) => (React.createElement("div", { key: `${left}_${width}_${idx}`, className: classes.highlight, style: {
47
+ .map(({ left, width, highlight, label }, idx) => (React.createElement("div", {
48
+ /* biome-ignore lint/suspicious/noArrayIndexKey: */
49
+ key: `${left}_${width}_${idx}`, className: classes.highlight, style: {
48
50
  left,
49
51
  width,
50
52
  background: highlight,
51
53
  } }, showBookmarkLabels ? (React.createElement(Tooltip, { title: label, arrow: true },
52
54
  React.createElement(BookmarkIcon, { fontSize: "small", sx: {
53
- color: `${colord(highlight).alpha() !== 0
55
+ color: colord(highlight).alpha() !== 0
54
56
  ? colord(highlight).alpha(0.8).toRgbString()
55
- : colord(highlight).alpha(0).toRgbString()}`,
57
+ : colord(highlight).alpha(0).toRgbString(),
56
58
  } }))) : null)))
57
59
  : null;
58
60
  });
package/esm/GridBookmarkWidget/components/Highlight/OverviewHighlight.js CHANGED
@@ -44,7 +44,7 @@ const OverviewHighlight = observer(function OverviewHighlight({ model, overview,
44
44
  .filter(notEmpty)
45
45
  .map((obj, idx) => {
46
46
  const { left, width, highlight, label } = obj;
47
- return (React.createElement(Tooltip, { key: JSON.stringify(obj) + '-' + idx, title: showBookmarkLabels ? label : '', arrow: true },
47
+ return (React.createElement(Tooltip, { key: `${JSON.stringify(obj)}-${idx}`, title: showBookmarkLabels ? label : '', arrow: true },
48
48
  React.createElement("div", { className: classes.highlight, style: {
49
49
  left,
50
50
  width,
package/esm/GridBookmarkWidget/components/Highlight/index.js CHANGED
@@ -5,18 +5,18 @@ import OverviewHighlight from './OverviewHighlight';
5
5
  export default function AddHighlightModelF(pluginManager) {
6
6
  pluginManager.addToExtensionPoint('LinearGenomeView-TracksContainerComponent',
7
7
  // @ts-expect-error
8
- (rest = [], { model }) => {
8
+ (rest, { model }) => {
9
9
  return [
10
- ...rest,
11
- React.createElement(Highlight, { key: `highlight_grid_bookmark`, model: model }),
10
+ ...(rest || []),
11
+ React.createElement(Highlight, { key: "highlight_grid_bookmark", model: model }),
12
12
  ];
13
13
  });
14
14
  pluginManager.addToExtensionPoint('LinearGenomeView-OverviewScalebarComponent',
15
15
  // @ts-expect-error
16
- (rest = [], { model, overview }) => {
16
+ (rest, { model, overview }) => {
17
17
  return [
18
- ...rest,
19
- React.createElement(OverviewHighlight, { key: `overview_highlight_grid_bookmark`, model: model, overview: overview }),
18
+ ...(rest || []),
19
+ React.createElement(OverviewHighlight, { key: "overview_highlight_grid_bookmark", model: model, overview: overview }),
20
20
  ];
21
21
  });
22
22
  }
package/esm/GridBookmarkWidget/components/dialogs/DeleteBookmarksDialog.js CHANGED
@@ -12,7 +12,9 @@ const DeleteBookmarksDialog = observer(function ({ onClose, model, }) {
12
12
  React.createElement("br", null),
13
13
  React.createElement("span", null, "Use the checkboxes to select individual bookmarks to delete."))) : ('Only selected bookmarks will be deleted.'))),
14
14
  React.createElement(DialogActions, null,
15
- React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => onClose() }, "Cancel"),
15
+ React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => {
16
+ onClose();
17
+ } }, "Cancel"),
16
18
  React.createElement(Button, { variant: "contained", color: "primary", onClick: () => {
17
19
  if (deleteAll) {
18
20
  model.clearAllBookmarks();
package/esm/GridBookmarkWidget/components/dialogs/EditBookmarkLabelDialog.js CHANGED
@@ -12,10 +12,12 @@ const EditBookmarkLabelDialog = observer(function ({ model, onClose, dialogRow,
12
12
  ' ',
13
13
  React.createElement("strong", null, assembleLocString(dialogRow.correspondingObj)),
14
14
  ":"),
15
- React.createElement(TextField, { fullWidth: true, inputProps: { 'data-testid': 'edit-bookmark-label-field' }, variant: "outlined", value: newLabel, onChange: e => setNewLabel(e.target.value), autoFocus: true })),
15
+ React.createElement(TextField, { fullWidth: true, inputProps: { 'data-testid': 'edit-bookmark-label-field' }, variant: "outlined", value: newLabel, onChange: e => {
16
+ setNewLabel(e.target.value);
17
+ }, autoFocus: true })),
16
18
  React.createElement(DialogActions, null,
17
19
  React.createElement(Button, { variant: "contained", color: "primary", onClick: () => {
18
- if (newLabel && dialogRow) {
20
+ if (newLabel) {
19
21
  model.updateBookmarkLabel(dialogRow, newLabel);
20
22
  }
21
23
  setNewLabel('');
package/esm/GridBookmarkWidget/components/dialogs/EditHighlightColorDialog.js CHANGED
@@ -12,9 +12,13 @@ const EditHighlightColorDialog = observer(function ({ onClose, model, }) {
12
12
  React.createElement(DialogContent, null,
13
13
  React.createElement(Typography, { variant: "h6" }, "Bulk highlight selector"),
14
14
  React.createElement(Alert, { severity: "info" }, editNone ? (React.createElement("span", null, "Use the checkboxes to select individual bookmarks to edit.")) : ('Only selected bookmarks will be edited.')),
15
- !editNone ? (React.createElement(ColorPicker, { color: color, onChange: event => setColor(event) })) : null),
15
+ !editNone ? (React.createElement(ColorPicker, { color: color, onChange: event => {
16
+ setColor(event);
17
+ } })) : null),
16
18
  React.createElement(DialogActions, null,
17
- React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => onClose() }, "Cancel"),
19
+ React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => {
20
+ onClose();
21
+ } }, "Cancel"),
18
22
  React.createElement(Button, { variant: "contained", color: "primary", onClick: () => {
19
23
  model.updateBulkBookmarkHighlights(color);
20
24
  onClose();
package/esm/GridBookmarkWidget/components/dialogs/ExportBookmarksDialog.js CHANGED
@@ -31,7 +31,9 @@ const ExportBookmarksDialog = observer(function ExportBookmarksDialog({ model, o
31
31
  React.createElement("span", null, "Use the checkboxes to select individual bookmarks to export."))) : ('Only selected bookmarks will be exported.')),
32
32
  React.createElement("div", { className: classes.flexItem },
33
33
  React.createElement(Typography, null, "Format to download:"),
34
- React.createElement(Select, { size: "small", value: fileType, onChange: event => setFileType(event.target.value) },
34
+ React.createElement(Select, { size: "small", value: fileType, onChange: event => {
35
+ setFileType(event.target.value);
36
+ } },
35
37
  React.createElement(MenuItem, { value: "BED" }, "BED"),
36
38
  React.createElement(MenuItem, { value: "TSV" }, "TSV")))),
37
39
  React.createElement(DialogActions, null,
package/esm/GridBookmarkWidget/components/dialogs/HighlightSettingsDialog.js CHANGED
@@ -17,6 +17,8 @@ const HighlightSettingsDialog = observer(function ({ onClose, model, }) {
17
17
  } }),
18
18
  React.createElement(Typography, null, "Toggle 'bookmark' icon on LGV tracks"))),
19
19
  React.createElement(DialogActions, null,
20
- React.createElement(Button, { variant: "contained", color: "primary", onClick: () => onClose() }, "Close"))));
20
+ React.createElement(Button, { variant: "contained", color: "primary", onClick: () => {
21
+ onClose();
22
+ } }, "Close"))));
21
23
  });
22
24
  export default HighlightSettingsDialog;
package/esm/GridBookmarkWidget/components/dialogs/ImportBookmarksDialog.js CHANGED
@@ -12,17 +12,14 @@ import ImportIcon from '@mui/icons-material/Publish';
12
12
  import ExpandMoreIcon from '@mui/icons-material/ExpandMore';
13
13
  import { fromUrlSafeB64 } from '../../utils';
14
14
  import { readSessionFromDynamo } from '../../sessionSharing';
15
- const useStyles = makeStyles()(theme => {
16
- var _a;
17
- return ({
18
- expandIcon: {
19
- color: ((_a = theme.palette.tertiary) === null || _a === void 0 ? void 0 : _a.contrastText) || '#fff',
20
- },
21
- minWidth: {
22
- minWidth: 500,
23
- },
24
- });
25
- });
15
+ const useStyles = makeStyles()(theme => ({
16
+ expandIcon: {
17
+ color: theme.palette.tertiary.contrastText || '#fff',
18
+ },
19
+ minWidth: {
20
+ minWidth: 500,
21
+ },
22
+ }));
26
23
  async function getBookmarksFromShareLink(shareLink, shareURL) {
27
24
  const defaultURL = 'https://share.jbrowse.org/api/v1/';
28
25
  const urlParams = new URL(shareLink);
@@ -47,7 +44,7 @@ async function getBookmarksFromTSVFile(lines) {
47
44
  const [refName, start, end, label, assemblyName] = line.split('\t');
48
45
  return {
49
46
  assemblyName: assemblyName,
50
- refName,
47
+ refName: refName,
51
48
  start: +start,
52
49
  end: +end,
53
50
  label: label === '.' ? undefined : label,
@@ -61,7 +58,7 @@ async function getBookmarksFromBEDFile(lines, selectedAsm) {
61
58
  const [refName, start, end, label] = line.split('\t');
62
59
  return {
63
60
  assemblyName: selectedAsm,
64
- refName,
61
+ refName: refName,
65
62
  start: +start,
66
63
  end: +end,
67
64
  label: label === '.' ? undefined : label,
@@ -79,18 +76,26 @@ const ImportBookmarksDialog = observer(function ({ onClose, model, }) {
79
76
  const [expanded, setExpanded] = useState('shareLinkAccordion');
80
77
  return (React.createElement(Dialog, { open: true, onClose: onClose, maxWidth: "xl", title: "Import bookmarks" },
81
78
  React.createElement(DialogContent, { className: classes.minWidth },
82
- React.createElement(Accordion, { expanded: expanded === 'shareLinkAccordion', onChange: () => setExpanded('shareLinkAccordion') },
79
+ React.createElement(Accordion, { expanded: expanded === 'shareLinkAccordion', onChange: () => {
80
+ setExpanded('shareLinkAccordion');
81
+ } },
83
82
  React.createElement(AccordionSummary, { expandIcon: React.createElement(ExpandMoreIcon, { className: classes.expandIcon }) },
84
83
  React.createElement(Typography, { style: { display: 'flex', alignItems: 'center', gap: '5px' } }, "Import from share link")),
85
84
  React.createElement(AccordionDetails, null,
86
85
  React.createElement(Typography, null, "Paste a bookmark share link generated by the 'Share' button from the bookmarks widget"),
87
- React.createElement(TextField, { label: "Enter Share URL", variant: "outlined", fullWidth: true, value: shareLink, onChange: e => setShareLink(e.target.value) }))),
88
- React.createElement(Accordion, { expanded: expanded === 'fileAccordion', onChange: () => setExpanded('fileAccordion') },
86
+ React.createElement(TextField, { label: "Enter Share URL", variant: "outlined", fullWidth: true, value: shareLink, onChange: e => {
87
+ setShareLink(e.target.value);
88
+ } }))),
89
+ React.createElement(Accordion, { expanded: expanded === 'fileAccordion', onChange: () => {
90
+ setExpanded('fileAccordion');
91
+ } },
89
92
  React.createElement(AccordionSummary, { expandIcon: React.createElement(ExpandMoreIcon, { className: classes.expandIcon }) },
90
93
  React.createElement(Typography, null, "Import from file")),
91
94
  React.createElement(AccordionDetails, null,
92
95
  React.createElement(FileSelector, { location: location, setLocation: setLocation, name: "File", description: `Choose a BED or TSV format file to import. Required TSV column headers are "chrom, start, end, label, assembly_name".` }),
93
- React.createElement(AssemblySelector, { onChange: val => setSelectedAsm(val), helperText: `Select the assembly for BED file.`, session: session, selected: selectedAsm }))),
96
+ React.createElement(AssemblySelector, { onChange: val => {
97
+ setSelectedAsm(val);
98
+ }, helperText: 'Select the assembly for BED file.', session: session, selected: selectedAsm }))),
94
99
  error ? React.createElement(ErrorMessage, { error: error }) : null),
95
100
  React.createElement(DialogActions, null,
96
101
  React.createElement(Button, { variant: "contained", color: "secondary", onClick: onClose }, "Cancel"),
package/esm/GridBookmarkWidget/components/dialogs/ShareBookmarksDialog.js CHANGED
@@ -26,7 +26,8 @@ const ShareBookmarksDialog = observer(function ({ onClose, model, }) {
26
26
  ? model.allBookmarksModel
27
27
  : model.sharedBookmarksModel;
28
28
  useEffect(() => {
29
- let cancelled = false;
29
+ // eslint-disable-next-line @typescript-eslint/no-floating-promises
30
+ ;
30
31
  (async () => {
31
32
  try {
32
33
  if (!isSessionWithShareURL(session)) {
@@ -36,14 +37,12 @@ const ShareBookmarksDialog = observer(function ({ onClose, model, }) {
36
37
  const snap = getSnapshot(bookmarksToShare);
37
38
  const locationUrl = new URL(window.location.href);
38
39
  const result = await shareSessionToDynamo(snap, session.shareURL, locationUrl.href);
39
- if (!cancelled) {
40
- const params = new URLSearchParams(locationUrl.search);
41
- params.set('bookmarks', `share-${result.json.sessionId}`);
42
- params.set('password', result.password);
43
- locationUrl.search = params.toString();
44
- setUrl(locationUrl.href);
45
- setLoading(false);
46
- }
40
+ const params = new URLSearchParams(locationUrl.search);
41
+ params.set('bookmarks', `share-${result.json.sessionId}`);
42
+ params.set('password', result.password);
43
+ locationUrl.search = params.toString();
44
+ setUrl(locationUrl.href);
45
+ setLoading(false);
47
46
  }
48
47
  catch (e) {
49
48
  setError(e);
@@ -52,9 +51,6 @@ const ShareBookmarksDialog = observer(function ({ onClose, model, }) {
52
51
  setLoading(false);
53
52
  }
54
53
  })();
55
- return () => {
56
- cancelled = true;
57
- };
58
54
  }, [bookmarksToShare, session]);
59
55
  return (React.createElement(Dialog, { open: true, onClose: onClose, title: "Share bookmarks" },
60
56
  React.createElement(DialogContent, { style: { display: 'flex', flexFlow: 'column', gap: '5px' } },
package/esm/GridBookmarkWidget/model.d.ts CHANGED
@@ -21,8 +21,8 @@ declare const LabeledRegionModel: import("mobx-state-tree").IModelType<{
21
21
  export interface IExtendedLGV extends LinearGenomeViewModel {
22
22
  showBookmarkHighlights: boolean;
23
23
  showBookmarkLabels: boolean;
24
- toggleShowBookmarkHighlights: (arg: boolean) => {};
25
- toggleShowBookmarkLabels: (arg: boolean) => {};
24
+ toggleShowBookmarkHighlights: (arg: boolean) => void;
25
+ toggleShowBookmarkLabels: (arg: boolean) => void;
26
26
  }
27
27
  export interface ILabeledRegionModel extends SnapshotIn<typeof LabeledRegionModel> {
28
28
  refName: string;
package/esm/GridBookmarkWidget/model.js CHANGED
@@ -158,7 +158,9 @@ export default function f(_pluginManager) {
158
158
  * #action
159
159
  */
160
160
  updateBulkBookmarkHighlights(color) {
161
- self.selectedBookmarks.forEach(bookmark => this.updateBookmarkHighlight(bookmark, color));
161
+ self.selectedBookmarks.forEach(bookmark => {
162
+ this.updateBookmarkHighlight(bookmark, color);
163
+ });
162
164
  },
163
165
  /**
164
166
  * #action
@@ -179,6 +181,7 @@ export default function f(_pluginManager) {
179
181
  const { views } = getSession(self);
180
182
  views.forEach(view => {
181
183
  var _a;
184
+ // @ts-expect-error
182
185
  (_a = view.toggleShowBookmarkHighlights) === null || _a === void 0 ? void 0 : _a.call(view, toggle);
183
186
  });
184
187
  },
@@ -189,6 +192,7 @@ export default function f(_pluginManager) {
189
192
  const { views } = getSession(self);
190
193
  views.forEach(view => {
191
194
  var _a;
195
+ // @ts-expect-error
192
196
  (_a = view.toggleShowBookmarkLabels) === null || _a === void 0 ? void 0 : _a.call(view, toggle);
193
197
  });
194
198
  },
package/esm/GridBookmarkWidget/utils.js CHANGED
@@ -38,9 +38,12 @@ export function downloadBookmarkFile(fileFormat, model) {
38
38
  const { label } = bookmark;
39
39
  const labelVal = label === '' ? '.' : label;
40
40
  const line = `${bookmark.refName}\t${bookmark.start}\t${bookmark.end}\t${labelVal}\n`;
41
- fileContents[bookmark.assemblyName]
42
- ? fileContents[bookmark.assemblyName].push(line)
43
- : (fileContents[bookmark.assemblyName] = [line]);
41
+ if (fileContents[bookmark.assemblyName]) {
42
+ fileContents[bookmark.assemblyName].push(line);
43
+ }
44
+ else {
45
+ fileContents[bookmark.assemblyName] = [line];
46
+ }
44
47
  });
45
48
  for (const assembly in fileContents) {
46
49
  const fileContent = fileContents[assembly].reduce((a, b) => a + b, fileHeader);
package/esm/index.js CHANGED
@@ -62,9 +62,8 @@ export default class GridBookmarkPlugin extends Plugin {
62
62
  navigateNewestBookmark() {
63
63
  const session = getSession(self);
64
64
  const bookmarkWidget = self.activateBookmarkWidget();
65
- const regions = bookmarkWidget.bookmarks;
66
- if (regions === null || regions === void 0 ? void 0 : regions.length) {
67
- self.navTo(regions.at(-1));
65
+ if (bookmarkWidget.bookmarks.length) {
66
+ self.navTo(bookmarkWidget.bookmarks.at(-1));
68
67
  }
69
68
  else {
70
69
  session.notify('There are no recent bookmarks to navigate to.', 'info');
@@ -74,7 +73,12 @@ export default class GridBookmarkPlugin extends Plugin {
74
73
  if (self.id === getSession(self).focusedViewId) {
75
74
  const selectedRegions = self.getSelectedRegions(undefined, undefined);
76
75
  const bookmarkWidget = self.activateBookmarkWidget();
77
- bookmarkWidget.addBookmark(selectedRegions[0]);
76
+ if (!selectedRegions.length) {
77
+ throw new Error('no region selected');
78
+ }
79
+ else {
80
+ bookmarkWidget.addBookmark(selectedRegions[0]);
81
+ }
78
82
  }
79
83
  },
80
84
  }))
@@ -98,21 +102,27 @@ export default class GridBookmarkPlugin extends Plugin {
98
102
  {
99
103
  label: 'Bookmark current region',
100
104
  icon: BookmarkIcon,
101
- onClick: () => self.bookmarkCurrentRegion(),
105
+ onClick: () => {
106
+ self.bookmarkCurrentRegion();
107
+ },
102
108
  },
103
109
  {
104
110
  label: 'Toggle bookmark highlights',
105
111
  icon: HighlightIcon,
106
112
  type: 'checkbox',
107
113
  checked: self.showBookmarkHighlights,
108
- onClick: () => self.toggleShowBookmarkHighlights(),
114
+ onClick: () => {
115
+ self.toggleShowBookmarkHighlights();
116
+ },
109
117
  },
110
118
  {
111
119
  label: 'Toggle bookmark labels',
112
120
  icon: LabelIcon,
113
121
  type: 'checkbox',
114
122
  checked: self.showBookmarkLabels,
115
- onClick: () => self.toggleShowBookmarkLabels(),
123
+ onClick: () => {
124
+ self.toggleShowBookmarkLabels();
125
+ },
116
126
  },
117
127
  ],
118
128
  },
@@ -128,7 +138,12 @@ export default class GridBookmarkPlugin extends Plugin {
128
138
  const { leftOffset, rightOffset } = self;
129
139
  const selectedRegions = self.getSelectedRegions(leftOffset, rightOffset);
130
140
  const bookmarkWidget = self.activateBookmarkWidget();
131
- bookmarkWidget.addBookmark(selectedRegions[0]);
141
+ if (!selectedRegions.length) {
142
+ throw new Error('no regions selected');
143
+ }
144
+ else {
145
+ bookmarkWidget.addBookmark(selectedRegions[0]);
146
+ }
132
147
  },
133
148
  },
134
149
  ];
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-grid-bookmark",
3
- "version": "2.13.1",
3
+ "version": "2.14.0",
4
4
  "description": "JBrowse 2 grid bookmark widget",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -24,7 +24,7 @@
24
24
  ],
25
25
  "scripts": {
26
26
  "build": "npm-run-all build:*",
27
- "test": "cd ../..; jest plugins/grid-bookmark",
27
+ "test": "cd ../..; jest --passWithNoTests plugins/grid-bookmark",
28
28
  "prepublishOnly": "yarn test",
29
29
  "prepack": "yarn build && yarn useDist",
30
30
  "postpack": "yarn useSrc",
@@ -59,5 +59,5 @@
59
59
  "distModule": "esm/index.js",
60
60
  "srcModule": "src/index.ts",
61
61
  "module": "esm/index.js",
62
- "gitHead": "fcebca71cc1d066654603e1a9accfa6c6d4f764d"
62
+ "gitHead": "9fb8231d932db40adf0a283081765431756c66ff"
63
63
  }