jbrowse-plugin-msaview 3.1.0 → 3.2.0

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Files changed (43) hide show
  1. package/dist/LaunchMsaView/components/BlastQuery/BlastAutomaticPanel.js +1 -1
  2. package/dist/LaunchMsaView/components/BlastQuery/BlastManualPanel.js +1 -1
  3. package/dist/LaunchMsaView/components/BlastQuery/blastLaunchView.js +6 -4
  4. package/dist/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.js +1 -1
  5. package/dist/LaunchMsaView/components/ManualMSALoader/launchView.js +4 -2
  6. package/dist/LaunchMsaView/components/OrthologQuery/OrthologPanel.js +1 -1
  7. package/dist/LaunchMsaView/components/OrthologQuery/orthologLaunchView.js +4 -2
  8. package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js +1 -1
  9. package/dist/LaunchMsaView/components/PreLoadedMSA/preCalculatedLaunchView.js +4 -2
  10. package/dist/LaunchMsaView/components/SubmitCancelActions.d.ts +4 -1
  11. package/dist/LaunchMsaView/components/SubmitCancelActions.js +34 -10
  12. package/dist/LaunchMsaView/components/SubmitCancelActions.test.d.ts +1 -0
  13. package/dist/LaunchMsaView/components/SubmitCancelActions.test.js +55 -0
  14. package/dist/LaunchMsaViewExtensionPoint/index.js +2 -2
  15. package/dist/index.js +4 -1
  16. package/dist/jbrowse-plugin-msaview.umd.production.min.js +28 -28
  17. package/dist/jbrowse-plugin-msaview.umd.production.min.js.map +4 -4
  18. package/dist/utils/launchMsaView.d.ts +19 -0
  19. package/dist/utils/launchMsaView.js +13 -0
  20. package/dist/utils/workspaces.d.ts +34 -0
  21. package/dist/utils/workspaces.js +100 -0
  22. package/dist/utils/workspaces.test.d.ts +1 -0
  23. package/dist/utils/workspaces.test.js +100 -0
  24. package/dist/version.d.ts +1 -1
  25. package/dist/version.js +1 -1
  26. package/package.json +4 -1
  27. package/src/LaunchMsaView/components/BlastQuery/BlastAutomaticPanel.tsx +1 -0
  28. package/src/LaunchMsaView/components/BlastQuery/BlastManualPanel.tsx +1 -0
  29. package/src/LaunchMsaView/components/BlastQuery/blastLaunchView.ts +7 -4
  30. package/src/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.tsx +1 -0
  31. package/src/LaunchMsaView/components/ManualMSALoader/launchView.ts +5 -2
  32. package/src/LaunchMsaView/components/OrthologQuery/OrthologPanel.tsx +1 -1
  33. package/src/LaunchMsaView/components/OrthologQuery/orthologLaunchView.ts +5 -2
  34. package/src/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.tsx +1 -0
  35. package/src/LaunchMsaView/components/PreLoadedMSA/preCalculatedLaunchView.ts +5 -2
  36. package/src/LaunchMsaView/components/SubmitCancelActions.test.tsx +95 -0
  37. package/src/LaunchMsaView/components/SubmitCancelActions.tsx +80 -22
  38. package/src/LaunchMsaViewExtensionPoint/index.ts +21 -2
  39. package/src/index.ts +4 -1
  40. package/src/utils/launchMsaView.ts +30 -0
  41. package/src/utils/workspaces.test.ts +132 -0
  42. package/src/utils/workspaces.ts +146 -0
  43. package/src/version.ts +1 -1
@@ -0,0 +1,19 @@
1
+ import type { MsaViewPlacement } from './workspaces';
2
+ import type { AbstractSessionModel } from '@jbrowse/core/util';
3
+ /**
4
+ * A launch, stated: what the view is, and where it goes. Everything but
5
+ * `placement` is a react-msaview or plugin-model snapshot property, passed
6
+ * through untouched so this never becomes a list that has to grow.
7
+ */
8
+ export interface MsaViewLaunchSpec extends Record<string, unknown> {
9
+ /** default `stack`, the only thing an embedded session can do */
10
+ placement?: MsaViewPlacement;
11
+ }
12
+ /**
13
+ * The one place a launch adds an MSA view -- the dialog's four tabs, the Add
14
+ * menu, and the `LaunchView-MsaView` extension point a session spec arrives on
15
+ * all come through here. Each of them used to run its own `addView` and none
16
+ * placed the result, which is how a launch from a gene feature landed stacked
17
+ * under the very genome view it was connected to.
18
+ */
19
+ export declare function launchMsaView(session: AbstractSessionModel, { placement, ...snapshot }: MsaViewLaunchSpec): import("@jbrowse/core/util").AbstractViewModel;
@@ -0,0 +1,13 @@
1
+ import { placeMsaView } from './workspaces';
2
+ /**
3
+ * The one place a launch adds an MSA view -- the dialog's four tabs, the Add
4
+ * menu, and the `LaunchView-MsaView` extension point a session spec arrives on
5
+ * all come through here. Each of them used to run its own `addView` and none
6
+ * placed the result, which is how a launch from a gene feature landed stacked
7
+ * under the very genome view it was connected to.
8
+ */
9
+ export function launchMsaView(session, { placement = 'stack', ...snapshot }) {
10
+ const view = session.addView('MsaView', { type: 'MsaView', ...snapshot });
11
+ placeMsaView(session, view.id, placement);
12
+ return view;
13
+ }
@@ -0,0 +1,34 @@
1
+ import type { AbstractSessionModel } from '@jbrowse/core/util';
2
+ /**
3
+ * Where a launched MSA view lands. Every launch names one of these and stops
4
+ * there, so a host that arranges views differently is one function to teach.
5
+ *
6
+ * stack append below whatever is on screen
7
+ * splitRight its own cell to the right, beside the view it is connected to
8
+ * newTab its own tab in the current cell
9
+ */
10
+ export type MsaViewPlacement = 'stack' | 'splitRight' | 'newTab';
11
+ /**
12
+ * What the dialog does unasked. Side-by-side, because a launch from a gene
13
+ * feature sets `connectedViewId`: the pair shares a hover and a highlight, and
14
+ * reads as a split. A session spec defaults to `stack` instead.
15
+ */
16
+ export declare const DEFAULT_LAUNCH_PLACEMENT: MsaViewPlacement;
17
+ export declare const LAUNCH_PLACEMENT_KEY = "msaView-launchPlacement";
18
+ export declare function resetWorkspacesWarning(): void;
19
+ /**
20
+ * Whether this host can honor anything other than `stack`. Silent: the dialog
21
+ * asks on every render, and only a launch is worth warning about.
22
+ */
23
+ export declare function sessionSupportsPlacement(session: AbstractSessionModel): boolean;
24
+ /**
25
+ * Put a freshly added view where the launch said to. `stack` is a placement
26
+ * rather than the absence of one, so no caller has to ask what host it is on.
27
+ */
28
+ export declare function placeMsaView(session: AbstractSessionModel, viewId: string, placement: MsaViewPlacement): void;
29
+ /**
30
+ * The dialog's own remembered choice — not the host's preferences system, which
31
+ * records whether the user likes workspaces and does not exist everywhere.
32
+ */
33
+ export declare function readLaunchPlacement(): MsaViewPlacement;
34
+ export declare function writeLaunchPlacement(placement: MsaViewPlacement): void;
@@ -0,0 +1,100 @@
1
+ const PLACEMENTS = ['stack', 'splitRight', 'newTab'];
2
+ /**
3
+ * What the dialog does unasked. Side-by-side, because a launch from a gene
4
+ * feature sets `connectedViewId`: the pair shares a hover and a highlight, and
5
+ * reads as a split. A session spec defaults to `stack` instead.
6
+ */
7
+ export const DEFAULT_LAUNCH_PLACEMENT = 'splitRight';
8
+ export const LAUNCH_PLACEMENT_KEY = 'msaView-launchPlacement';
9
+ function hasAction(session, name) {
10
+ return (name in session &&
11
+ typeof session[name] === 'function');
12
+ }
13
+ // Warned at most once. This is a property of the host, so the answer is the
14
+ // same on every launch and a dialog the user reopens should not stack up noise.
15
+ let warnedPartial = false;
16
+ export function resetWorkspacesWarning() {
17
+ warnedPartial = false;
18
+ }
19
+ /**
20
+ * Whether this host can honor anything other than `stack`. Silent: the dialog
21
+ * asks on every render, and only a launch is worth warning about.
22
+ */
23
+ export function sessionSupportsPlacement(session) {
24
+ return (hasAction(session, 'setUseWorkspaces') &&
25
+ hasAction(session, 'setPendingMove'));
26
+ }
27
+ function isSessionWithWorkspaces(session) {
28
+ const canEnable = hasAction(session, 'setUseWorkspaces');
29
+ const canPlace = hasAction(session, 'setPendingMove');
30
+ // Missing BOTH is an embedded session: it has no workspaces, there is nothing
31
+ // to ask for, and silence is the right answer.
32
+ //
33
+ // Missing ONE is a host that has workspaces but places views some other way,
34
+ // and silence there is how the same feature broke in jbrowse-plugin-protein3d
35
+ // — jbrowse-web folded `setPendingMove` into its layout `init`, the guard went
36
+ // false, and the plugin simply stopped asking: no error, no missing feature,
37
+ // two views quietly stacking, nobody noticed for weeks. Feature detection
38
+ // cannot ask a host to announce a change, but it can tell "not supported here"
39
+ // from "supported, and gone".
40
+ //
41
+ // Two very different hosts produce this one shape and nothing on the session
42
+ // tells them apart, so the message carries both rather than a guess:
43
+ //
44
+ // - releases through v4.3.0, where placement is `setPendingMoveToSplitRight`,
45
+ // a module function in @jbrowse/app-core rather than a session action.
46
+ // Nothing is wrong and nothing needs fixing
47
+ // - a newer host that moved the action out from under us, which is the
48
+ // regression this warning exists to catch
49
+ //
50
+ // Do not quiet the first case by sniffing the version. The alarm is only worth
51
+ // having if it fires on a shape it cannot explain, and these two are identical.
52
+ if (canEnable !== canPlace && !warnedPartial) {
53
+ warnedPartial = true;
54
+ console.warn(`jbrowse-plugin-msaview: this session supports workspaces but not ` +
55
+ `${canPlace ? 'setUseWorkspaces' : 'setPendingMove'}, so the MSA view ` +
56
+ `was stacked instead of tiled. Expected on releases through v4.3.0, ` +
57
+ `which place views through @jbrowse/app-core instead; on a newer host ` +
58
+ `it means the session API moved and the plugin needs updating to match.`);
59
+ }
60
+ return canEnable && canPlace;
61
+ }
62
+ /**
63
+ * Put a freshly added view where the launch said to. `stack` is a placement
64
+ * rather than the absence of one, so no caller has to ask what host it is on.
65
+ */
66
+ export function placeMsaView(session, viewId, placement) {
67
+ if (placement === 'stack' || !isSessionWithWorkspaces(session)) {
68
+ return;
69
+ }
70
+ session.setPendingMove({ type: placement, viewId });
71
+ // Session-scoped: turning workspaces on for this session leaves the user's
72
+ // own default alone, which is what `setUseWorkspaces` (as against
73
+ // `setUseWorkspacesPreference`) is for.
74
+ session.setUseWorkspaces(true);
75
+ }
76
+ function isPlacement(value) {
77
+ return PLACEMENTS.includes(value);
78
+ }
79
+ /**
80
+ * The dialog's own remembered choice — not the host's preferences system, which
81
+ * records whether the user likes workspaces and does not exist everywhere.
82
+ */
83
+ export function readLaunchPlacement() {
84
+ try {
85
+ const stored = globalThis.localStorage.getItem(LAUNCH_PLACEMENT_KEY);
86
+ return isPlacement(stored) ? stored : DEFAULT_LAUNCH_PLACEMENT;
87
+ }
88
+ catch (error) {
89
+ console.error(error);
90
+ return DEFAULT_LAUNCH_PLACEMENT;
91
+ }
92
+ }
93
+ export function writeLaunchPlacement(placement) {
94
+ try {
95
+ globalThis.localStorage.setItem(LAUNCH_PLACEMENT_KEY, placement);
96
+ }
97
+ catch (error) {
98
+ console.error(error);
99
+ }
100
+ }
@@ -0,0 +1 @@
1
+ export {};
@@ -0,0 +1,100 @@
1
+ import { afterEach, beforeEach, expect, test, vi } from 'vitest';
2
+ import { launchMsaView } from './launchMsaView';
3
+ import { DEFAULT_LAUNCH_PLACEMENT, LAUNCH_PLACEMENT_KEY, placeMsaView, readLaunchPlacement, resetWorkspacesWarning, sessionSupportsPlacement, writeLaunchPlacement, } from './workspaces';
4
+ function makeSession({ canPlace = true, canEnable = true, } = {}) {
5
+ const recorded = { moves: [], workspaces: [], added: [] };
6
+ const session = {
7
+ addView(type, snapshot) {
8
+ recorded.added.push({ type, snapshot });
9
+ return { id: `view-${recorded.added.length}` };
10
+ },
11
+ };
12
+ if (canPlace) {
13
+ session.setPendingMove = (move) => recorded.moves.push(move);
14
+ }
15
+ if (canEnable) {
16
+ session.setUseWorkspaces = (on) => recorded.workspaces.push(on);
17
+ }
18
+ return { session: session, recorded };
19
+ }
20
+ // node has no localStorage, and the plugin runs in a browser -- a Map-backed
21
+ // stub keeps read/write round-tripping without pulling in jsdom
22
+ function stubStorage() {
23
+ const store = new Map();
24
+ vi.stubGlobal('localStorage', {
25
+ getItem: (key) => store.get(key) ?? null,
26
+ setItem: (key, value) => store.set(key, value),
27
+ });
28
+ }
29
+ beforeEach(() => {
30
+ resetWorkspacesWarning();
31
+ stubStorage();
32
+ });
33
+ afterEach(() => {
34
+ vi.restoreAllMocks();
35
+ vi.unstubAllGlobals();
36
+ });
37
+ test('stack places nothing, on a host that could tile', () => {
38
+ const { session, recorded } = makeSession();
39
+ placeMsaView(session, 'view-1', 'stack');
40
+ expect(recorded.moves).toEqual([]);
41
+ expect(recorded.workspaces).toEqual([]);
42
+ });
43
+ test('splitRight asks for the move, then turns workspaces on', () => {
44
+ const { session, recorded } = makeSession();
45
+ placeMsaView(session, 'view-1', 'splitRight');
46
+ expect(recorded.moves).toEqual([{ type: 'splitRight', viewId: 'view-1' }]);
47
+ expect(recorded.workspaces).toEqual([true]);
48
+ });
49
+ test('newTab is the same path with the other move type', () => {
50
+ const { session, recorded } = makeSession();
51
+ placeMsaView(session, 'view-1', 'newTab');
52
+ expect(recorded.moves).toEqual([{ type: 'newTab', viewId: 'view-1' }]);
53
+ });
54
+ // an embedded session has no workspaces at all, so there is nothing to report
55
+ test('a session with neither action is a silent no-op', () => {
56
+ const warn = vi.spyOn(console, 'warn').mockImplementation(() => { });
57
+ const { session, recorded } = makeSession({
58
+ canPlace: false,
59
+ canEnable: false,
60
+ });
61
+ placeMsaView(session, 'view-1', 'splitRight');
62
+ expect(recorded.moves).toEqual([]);
63
+ expect(warn).not.toHaveBeenCalled();
64
+ expect(sessionSupportsPlacement(session)).toBe(false);
65
+ });
66
+ // the shape that broke jbrowse-plugin-protein3d silently: workspaces are there,
67
+ // the action this plugin reaches for is not
68
+ test('a half-supported host warns once and stacks', () => {
69
+ const warn = vi.spyOn(console, 'warn').mockImplementation(() => { });
70
+ const { session, recorded } = makeSession({ canPlace: false });
71
+ placeMsaView(session, 'view-1', 'splitRight');
72
+ placeMsaView(session, 'view-2', 'splitRight');
73
+ expect(recorded.moves).toEqual([]);
74
+ expect(warn).toHaveBeenCalledTimes(1);
75
+ expect(warn.mock.calls[0]?.[0]).toContain('setPendingMove');
76
+ });
77
+ test('the dialog default is side-by-side, and a junk value falls back to it', () => {
78
+ expect(DEFAULT_LAUNCH_PLACEMENT).toBe('splitRight');
79
+ expect(readLaunchPlacement()).toBe('splitRight');
80
+ localStorage.setItem(LAUNCH_PLACEMENT_KEY, 'sideways');
81
+ expect(readLaunchPlacement()).toBe('splitRight');
82
+ writeLaunchPlacement('stack');
83
+ expect(readLaunchPlacement()).toBe('stack');
84
+ });
85
+ test('launchMsaView defaults to stack, so a spec written before placement existed is unchanged', () => {
86
+ const { session, recorded } = makeSession();
87
+ launchMsaView(session, { data: { msa: '>a\nAC' } });
88
+ expect(recorded.added).toEqual([
89
+ { type: 'MsaView', snapshot: { type: 'MsaView', data: { msa: '>a\nAC' } } },
90
+ ]);
91
+ expect(recorded.moves).toEqual([]);
92
+ });
93
+ // placement is a launch instruction, not view state: MST would drop it from the
94
+ // snapshot without a word, and the view would land stacked with nothing said
95
+ test('launchMsaView keeps placement out of the view snapshot', () => {
96
+ const { session, recorded } = makeSession();
97
+ launchMsaView(session, { placement: 'splitRight', colWidth: 10 });
98
+ expect(recorded.added[0]?.snapshot).toEqual({ type: 'MsaView', colWidth: 10 });
99
+ expect(recorded.moves).toEqual([{ type: 'splitRight', viewId: 'view-1' }]);
100
+ });
package/dist/version.d.ts CHANGED
@@ -1 +1 @@
1
- export declare const version = "3.1.0";
1
+ export declare const version = "3.2.0";
package/dist/version.js CHANGED
@@ -1 +1 @@
1
- export const version = '3.1.0';
1
+ export const version = '3.2.0';
package/package.json CHANGED
@@ -1,5 +1,5 @@
1
1
  {
2
- "version": "3.1.0",
2
+ "version": "3.2.0",
3
3
  "license": "MIT",
4
4
  "name": "jbrowse-plugin-msaview",
5
5
  "repository": {
@@ -32,6 +32,8 @@
32
32
  "@mui/material": "^9.2.0",
33
33
  "@mui/system": "^9.2.0",
34
34
  "@mui/x-data-grid": "^9.10.0",
35
+ "@testing-library/dom": "^10.4.1",
36
+ "@testing-library/react": "^16.3.2",
35
37
  "@types/node": "^26.1.1",
36
38
  "@types/react": "^19.2.17",
37
39
  "esbuild": "^0.28.1",
@@ -41,6 +43,7 @@
41
43
  "eslint-plugin-react-hooks": "^7.1.1",
42
44
  "eslint-plugin-unicorn": "^72.0.0",
43
45
  "git-cliff": "^2.13.1",
46
+ "jsdom": "^30.0.1",
44
47
  "mobx": "^6.16.1",
45
48
  "mobx-react": "^9.2.2",
46
49
  "msa-parsers": "^6.0.0",
@@ -123,6 +123,7 @@ const BlastAutomaticPanel = observer(function ({
123
123
  ) : null}
124
124
  </LaunchPanelContent>
125
125
  <SubmitCancelActions
126
+ model={model}
126
127
  submitDisabled={!proteinSequence}
127
128
  onSubmit={() => {
128
129
  try {
@@ -155,6 +155,7 @@ const BlastManualPanel = observer(function ({
155
155
  </LaunchPanelContent>
156
156
 
157
157
  <SubmitCancelActions
158
+ model={model}
158
159
  submitDisabled={!selectedTranscript || !msaText.trim()}
159
160
  onSubmit={() => {
160
161
  try {
@@ -1,5 +1,8 @@
1
1
  import { getSession } from '@jbrowse/core/util'
2
2
 
3
+ import { launchMsaView } from '../../../utils/launchMsaView'
4
+ import { readLaunchPlacement } from '../../../utils/workspaces'
5
+
3
6
  import type { BlastParams } from '../../../MsaViewPanel/model'
4
7
  import type { CachedBlastResult } from '../../../utils/blastCache'
5
8
  import type { Feature } from '@jbrowse/core/util'
@@ -16,8 +19,8 @@ export function blastLaunchView({
16
19
  feature: Feature
17
20
  blastParams: BlastParams
18
21
  }) {
19
- getSession(view).addView('MsaView', {
20
- type: 'MsaView',
22
+ launchMsaView(getSession(view), {
23
+ placement: readLaunchPlacement(),
21
24
  displayName: newViewTitle,
22
25
  connectedViewId: view.id,
23
26
  connectedFeature: feature.toJSON(),
@@ -39,8 +42,8 @@ export function blastLaunchViewFromCache({
39
42
  cached: CachedBlastResult
40
43
  connectedFeature?: ReturnType<Feature['toJSON']>
41
44
  }) {
42
- getSession(view).addView('MsaView', {
43
- type: 'MsaView',
45
+ launchMsaView(getSession(view), {
46
+ placement: readLaunchPlacement(),
44
47
  displayName: newViewTitle,
45
48
  connectedViewId: view.id,
46
49
  connectedFeature,
@@ -137,6 +137,7 @@ const ManualMSALoader = observer(function PreLoadedMSA2({
137
137
  </LaunchPanelContent>
138
138
 
139
139
  <SubmitCancelActions
140
+ model={model}
140
141
  submitDisabled={
141
142
  !selectedTranscript ||
142
143
  (inputMethod === 'file' && !msaFileLocation) ||
@@ -1,5 +1,8 @@
1
1
  import { getSession } from '@jbrowse/core/util'
2
2
 
3
+ import { launchMsaView } from '../../../utils/launchMsaView'
4
+ import { readLaunchPlacement } from '../../../utils/workspaces'
5
+
3
6
  import type { Feature, FileLocation } from '@jbrowse/core/util'
4
7
  import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
5
8
 
@@ -23,8 +26,8 @@ export function launchView({
23
26
  tree?: string
24
27
  }
25
28
  }) {
26
- getSession(view).addView('MsaView', {
27
- type: 'MsaView',
29
+ launchMsaView(getSession(view), {
30
+ placement: readLaunchPlacement(),
28
31
  displayName: newViewTitle,
29
32
  connectedViewId: view.id,
30
33
  connectedFeature: feature.toJSON(),
@@ -98,9 +98,9 @@ const OrthologPanel = observer(function ({
98
98
  </div>
99
99
 
100
100
  <TranscriptSelector feature={feature} {...transcriptSelection} />
101
-
102
101
  </LaunchPanelContent>
103
102
  <SubmitCancelActions
103
+ model={model}
104
104
  submitDisabled={!proteinSequence || !rowCountValid}
105
105
  onSubmit={() => {
106
106
  try {
@@ -1,5 +1,8 @@
1
1
  import { getSession } from '@jbrowse/core/util'
2
2
 
3
+ import { launchMsaView } from '../../../utils/launchMsaView'
4
+ import { readLaunchPlacement } from '../../../utils/workspaces'
5
+
3
6
  import type { OrthologParams } from '../../../MsaViewPanel/model'
4
7
  import type { Feature } from '@jbrowse/core/util'
5
8
  import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
@@ -15,8 +18,8 @@ export function orthologLaunchView({
15
18
  feature: Feature
16
19
  orthologParams: OrthologParams
17
20
  }) {
18
- getSession(view).addView('MsaView', {
19
- type: 'MsaView',
21
+ launchMsaView(getSession(view), {
22
+ placement: readLaunchPlacement(),
20
23
  displayName: newViewTitle,
21
24
  connectedViewId: view.id,
22
25
  connectedFeature: feature.toJSON(),
@@ -130,6 +130,7 @@ const PreLoadedMSA = observer(function ({
130
130
  </LaunchPanelContent>
131
131
 
132
132
  <SubmitCancelActions
133
+ model={model}
133
134
  submitDisabled={!selectedTranscript || !msaData?.length}
134
135
  onSubmit={() => {
135
136
  try {
@@ -1,5 +1,8 @@
1
1
  import { getSession } from '@jbrowse/core/util'
2
2
 
3
+ import { launchMsaView } from '../../../utils/launchMsaView'
4
+ import { readLaunchPlacement } from '../../../utils/workspaces'
5
+
3
6
  import type { Feature } from '@jbrowse/core/util'
4
7
  import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
5
8
 
@@ -16,8 +19,8 @@ export function preCalculatedLaunchView({
16
19
  feature: Feature
17
20
  querySeqName: string
18
21
  }) {
19
- getSession(view).addView('MsaView', {
20
- type: 'MsaView',
22
+ launchMsaView(getSession(view), {
23
+ placement: readLaunchPlacement(),
21
24
  displayName: newViewTitle,
22
25
  treeAreaWidth: 200,
23
26
  querySeqName,
@@ -0,0 +1,95 @@
1
+ // @vitest-environment jsdom
2
+ import React from 'react'
3
+
4
+ import { cleanup, render, screen } from '@testing-library/react'
5
+ import { afterEach, beforeEach, expect, test, vi } from 'vitest'
6
+
7
+ import SubmitCancelActions from './SubmitCancelActions'
8
+ import { LAUNCH_PLACEMENT_KEY } from '../../utils/workspaces'
9
+
10
+ import type { AbstractTrackModel } from '@jbrowse/core/util'
11
+
12
+ // getSession walks the MST tree, and this component only wants the two actions
13
+ // off the far end of that walk
14
+ vi.mock('@jbrowse/core/util', () => ({
15
+ getSession: (model: { session: unknown }) => model.session,
16
+ }))
17
+
18
+ function trackModel(session: Record<string, unknown>) {
19
+ return { session } as unknown as AbstractTrackModel
20
+ }
21
+
22
+ const tiling = { setUseWorkspaces() {}, setPendingMove() {} }
23
+
24
+ beforeEach(() => {
25
+ localStorage.clear()
26
+ })
27
+
28
+ afterEach(() => {
29
+ cleanup()
30
+ })
31
+
32
+ function toggle() {
33
+ return screen.queryByRole('checkbox')
34
+ }
35
+
36
+ test('a host that can tile offers the choice, checked by default', () => {
37
+ render(
38
+ <SubmitCancelActions
39
+ model={trackModel(tiling)}
40
+ onSubmit={() => {}}
41
+ onCancel={() => {}}
42
+ />,
43
+ )
44
+ expect(toggle()).toBeTruthy()
45
+ expect((toggle() as HTMLInputElement).checked).toBe(true)
46
+ expect(localStorage.getItem(LAUNCH_PLACEMENT_KEY)).toBeNull()
47
+ })
48
+
49
+ // the box would do nothing on an embedded session, and a control that silently
50
+ // does nothing is worse than one that is not there
51
+ test('a host that cannot tile does not offer it', () => {
52
+ render(
53
+ <SubmitCancelActions
54
+ model={trackModel({})}
55
+ onSubmit={() => {}}
56
+ onCancel={() => {}}
57
+ />,
58
+ )
59
+ expect(toggle()).toBeNull()
60
+ expect(screen.getByText('Submit')).toBeTruthy()
61
+ })
62
+
63
+ test('a panel that launches nothing passes no model, and gets no box', () => {
64
+ render(<SubmitCancelActions onSubmit={() => {}} onCancel={() => {}} />)
65
+ expect(toggle()).toBeNull()
66
+ })
67
+
68
+ test('clicking it writes the placement the next launch will read', () => {
69
+ render(
70
+ <SubmitCancelActions
71
+ model={trackModel(tiling)}
72
+ onSubmit={() => {}}
73
+ onCancel={() => {}}
74
+ />,
75
+ )
76
+ toggle()!.click()
77
+ expect(localStorage.getItem(LAUNCH_PLACEMENT_KEY)).toBe('stack')
78
+ expect((toggle() as HTMLInputElement).checked).toBe(false)
79
+
80
+ toggle()!.click()
81
+ expect(localStorage.getItem(LAUNCH_PLACEMENT_KEY)).toBe('splitRight')
82
+ expect((toggle() as HTMLInputElement).checked).toBe(true)
83
+ })
84
+
85
+ test('a stored choice is what the box opens on', () => {
86
+ localStorage.setItem(LAUNCH_PLACEMENT_KEY, 'stack')
87
+ render(
88
+ <SubmitCancelActions
89
+ model={trackModel(tiling)}
90
+ onSubmit={() => {}}
91
+ onCancel={() => {}}
92
+ />,
93
+ )
94
+ expect((toggle() as HTMLInputElement).checked).toBe(false)
95
+ })
@@ -1,6 +1,53 @@
1
- import React from 'react'
1
+ import React, { useState } from 'react'
2
2
 
3
- import { Button, DialogActions } from '@mui/material'
3
+ import { getSession } from '@jbrowse/core/util'
4
+ import {
5
+ Button,
6
+ Checkbox,
7
+ DialogActions,
8
+ FormControlLabel,
9
+ } from '@mui/material'
10
+
11
+ import {
12
+ readLaunchPlacement,
13
+ sessionSupportsPlacement,
14
+ writeLaunchPlacement,
15
+ } from '../../utils/workspaces'
16
+
17
+ import type { AbstractTrackModel } from '@jbrowse/core/util'
18
+
19
+ /**
20
+ * Where the launch puts the view, offered wherever a launch is submitted.
21
+ *
22
+ * A checkbox rather than a menu of the three placements: the choice a reader
23
+ * has at this point is "beside the genome view or under it", and `newTab` is a
24
+ * spec's to state, not a thing to pick before you have seen the alignment.
25
+ *
26
+ * Absent entirely on a host that cannot tile — an embedded session, or a
27
+ * release that places views its own way — because the box would do nothing
28
+ * there and every launch would quietly ignore it.
29
+ */
30
+ function PlacementToggle({ model }: { model: AbstractTrackModel }) {
31
+ const session = getSession(model)
32
+ const [sideBySide, setSideBySide] = useState(
33
+ () => readLaunchPlacement() === 'splitRight',
34
+ )
35
+ return sessionSupportsPlacement(session) ? (
36
+ <FormControlLabel
37
+ label="Open beside the genome view"
38
+ control={
39
+ <Checkbox
40
+ checked={sideBySide}
41
+ onChange={event => {
42
+ const { checked } = event.target
43
+ setSideBySide(checked)
44
+ writeLaunchPlacement(checked ? 'splitRight' : 'stack')
45
+ }}
46
+ />
47
+ }
48
+ />
49
+ ) : null
50
+ }
4
51
 
5
52
  export default function SubmitCancelActions({
6
53
  onSubmit,
@@ -8,34 +55,45 @@ export default function SubmitCancelActions({
8
55
  submitDisabled,
9
56
  submitLabel = 'Submit',
10
57
  cancelLabel = 'Cancel',
58
+ model,
11
59
  }: {
12
60
  onSubmit: () => void
13
61
  onCancel: () => void
14
62
  submitDisabled?: boolean
15
63
  submitLabel?: string
16
64
  cancelLabel?: string
65
+ /** omitted by a panel that submits something other than a view launch */
66
+ model?: AbstractTrackModel
17
67
  }) {
18
68
  return (
19
- <DialogActions>
20
- <Button
21
- color="primary"
22
- variant="contained"
23
- disabled={submitDisabled}
24
- onClick={() => {
25
- onSubmit()
26
- }}
27
- >
28
- {submitLabel}
29
- </Button>
30
- <Button
31
- color="secondary"
32
- variant="contained"
33
- onClick={() => {
34
- onCancel()
35
- }}
36
- >
37
- {cancelLabel}
38
- </Button>
69
+ // The buttons are one child rather than two, so a dialog too narrow for
70
+ // the whole row wraps them together underneath the option instead of
71
+ // breaking Cancel away from Submit or shrinking both out of shape.
72
+ <DialogActions sx={{ flexWrap: 'wrap', rowGap: 1 }}>
73
+ {model ? <PlacementToggle model={model} /> : null}
74
+ <div style={{ display: 'flex', gap: 8, marginLeft: 'auto' }}>
75
+ <Button
76
+ sx={{ flexShrink: 0 }}
77
+ color="primary"
78
+ variant="contained"
79
+ disabled={submitDisabled}
80
+ onClick={() => {
81
+ onSubmit()
82
+ }}
83
+ >
84
+ {submitLabel}
85
+ </Button>
86
+ <Button
87
+ sx={{ flexShrink: 0 }}
88
+ color="secondary"
89
+ variant="contained"
90
+ onClick={() => {
91
+ onCancel()
92
+ }}
93
+ >
94
+ {cancelLabel}
95
+ </Button>
96
+ </div>
39
97
  </DialogActions>
40
98
  )
41
99
  }