@jbrowse/product-core 5.0.0-beta.2 → 5.0.0-beta.3

package/esm/RootModel/BaseRootModel.js

@@ -1,9 +1,9 @@
 import TextSearchManager from '@jbrowse/core/TextSearch/TextSearchManager';
 import assemblyManagerFactory from '@jbrowse/core/assemblyManager';
 import RpcManager from '@jbrowse/core/rpc/RpcManager';
+import { scheduleDetachedDestroy } from '@jbrowse/core/util';
 import { cast, detach, getType, isStateTreeNode, types, } from '@jbrowse/mobx-state-tree';
 import { describeUnbuildableNodes, pruneUnbuildableNodes, } from '../pruneUnbuildableNodes.js';
-import { scheduleDetachedDestroy } from '../scheduleDetachedDestroy.js';
 import { migrateSessionSnapshot } from '../sessionMigrations/index.js';
 import { filterSessionInPlace } from '../sessionUtils.js';
 // `session` is a `types.maybe(sessionModelType)` where `sessionModelType` is the

package/esm/Session/BaseSession.d.ts

@@ -162,11 +162,8 @@ export declare function BaseSessionModel<ROOT_MODEL_TYPE extends BaseRootModelTy
      * `{ displayType, slot, value }` — the inventory the Preferences dialog
      * lists and clears one at a time (`setDisplayTypeDefault(…, undefined)`).
      *
-     * Here rather than filtered out of `getPreferenceChanges` by the dialog,
-     * because the composite-key layout is this file's: a consumer that
-     * recognized these rows by matching the path head is exactly the coupling
-     * `DISPLAY_TYPE_DEFAULTS_PATH_HEAD` stopped being exported over, where a
-     * rename on one side alone silently no-ops the other.
+     * Parsed here rather than by the dialog, because the composite-key
+     * layout is this file's and nothing outside it should depend on it.
      */
     getDisplayTypeDefaults(): {
         displayType: string;
@@ -175,14 +172,13 @@ export declare function BaseSessionModel<ROOT_MODEL_TYPE extends BaseRootModelTy
     }[];
     /**
      * #method
-     * every runtime preference-override that currently differs from its
-     * config/admin default, as `{ path, from, to }` rows — the exact set
-     * `clearPreferenceOverrides` reverts. Backs the confirmation diff shown
-     * before "Reset to defaults" (mirrors the per-track changes dialog). A
-     * scalar pref (animationMode, scrollZoom) whose override equals the
-     * default is omitted (reverting it is a no-op); each promoted
-     * per-display-type default is always a difference from the un-promoted
-     * state, so `from` reads "(default)".
+     * every scalar preference override that currently differs from its
+     * config/admin default, as `{ path, from, to }` rows whose path is the
+     * override's own key. A scalar pref (animationMode, scrollZoom) whose
+     * override equals the default is omitted, since reverting it is a no-op.
+     * Promoted display-type defaults share the map but are not here: they
+     * are `getDisplayTypeDefaults`, and the Preferences dialog lists them
+     * through one builder on both of its surfaces.
      */
     getPreferenceChanges(): TrackConfigChange[];
 } & {
@@ -261,19 +257,6 @@ export declare function BaseSessionModel<ROOT_MODEL_TYPE extends BaseRootModelTy
      * Preferences dialog "Reset to defaults" confirmation.
      */
     clearPreferenceOverride(key: string): void;
-    /**
-     * #action
-     * revert one row emitted by `getPreferenceChanges`, addressed by its
-     * display `path`. Backs the per-entry reset in the Preferences dialog's
-     * "Reset to defaults" confirmation.
-     *
-     * Lives here rather than in that dialog because this model owns both path
-     * shapes it has to undo: a promoted per-display-type default, whose row
-     * path is a readable label over a flat composite storage key, and every
-     * other override, whose path *is* its key. The dialog used to re-derive
-     * the first case from an exported path-head constant.
-     */
-    resetPreferenceChange(path: string[]): void;
     /**
      * #action
      * set the global scroll-to-zoom preference (see the `scrollZoom` getter)

package/esm/Session/BaseSession.js

@@ -39,18 +39,6 @@ function parseDisplayTypeDefaultKey(key) {
     const [displayType, slot] = rest.split('\0');
     return displayType && slot ? { displayType, slot } : undefined;
 }
-// Head of the display path a promoted default takes in a `getPreferenceChanges`
-// row: `[DISPLAY_TYPE_DEFAULTS_PATH_HEAD, displayType, slot]`. Purely a
-// readable row label, deliberately distinct from the flat
-// `DISPLAY_TYPE_DEFAULT_PREFIX` storage key above.
-//
-// Module-private, like the storage key: both the producer
-// (`getPreferenceChanges`) and the consumer (`resetPreferenceChange`) are
-// methods on this model, so the two path shapes this file emits are the only
-// ones it has to undo. It used to be exported for the Preferences dialog to
-// match on and re-route back through `setDisplayTypeDefault`, which meant a
-// rename on one side alone would silently no-op that dialog's per-row reset.
-const DISPLAY_TYPE_DEFAULTS_PATH_HEAD = 'displayTypeDefaults';
 /**
  * #stateModel BaseSessionModel
  *
@@ -245,11 +233,8 @@ export function BaseSessionModel(_pluginManager) {
          * `{ displayType, slot, value }` — the inventory the Preferences dialog
          * lists and clears one at a time (`setDisplayTypeDefault(…, undefined)`).
          *
-         * Here rather than filtered out of `getPreferenceChanges` by the dialog,
-         * because the composite-key layout is this file's: a consumer that
-         * recognized these rows by matching the path head is exactly the coupling
-         * `DISPLAY_TYPE_DEFAULTS_PATH_HEAD` stopped being exported over, where a
-         * rename on one side alone silently no-ops the other.
+         * Parsed here rather than by the dialog, because the composite-key
+         * layout is this file's and nothing outside it should depend on it.
          */
         getDisplayTypeDefaults() {
             const found = [];
@@ -263,31 +248,18 @@ export function BaseSessionModel(_pluginManager) {
         },
         /**
          * #method
-         * every runtime preference-override that currently differs from its
-         * config/admin default, as `{ path, from, to }` rows — the exact set
-         * `clearPreferenceOverrides` reverts. Backs the confirmation diff shown
-         * before "Reset to defaults" (mirrors the per-track changes dialog). A
-         * scalar pref (animationMode, scrollZoom) whose override equals the
-         * default is omitted (reverting it is a no-op); each promoted
-         * per-display-type default is always a difference from the un-promoted
-         * state, so `from` reads "(default)".
+         * every scalar preference override that currently differs from its
+         * config/admin default, as `{ path, from, to }` rows whose path is the
+         * override's own key. A scalar pref (animationMode, scrollZoom) whose
+         * override equals the default is omitted, since reverting it is a no-op.
+         * Promoted display-type defaults share the map but are not here: they
+         * are `getDisplayTypeDefaults`, and the Preferences dialog lists them
+         * through one builder on both of its surfaces.
          */
         getPreferenceChanges() {
             const changes = [];
             for (const [key, value] of self.preferencesOverrides.entries()) {
-                const dtd = parseDisplayTypeDefaultKey(key);
-                if (dtd) {
-                    changes.push({
-                        path: [
-                            DISPLAY_TYPE_DEFAULTS_PATH_HEAD,
-                            dtd.displayType,
-                            dtd.slot,
-                        ],
-                        from: undefined,
-                        to: value,
-                    });
-                }
-                else {
+                if (!key.startsWith(DISPLAY_TYPE_DEFAULT_PREFIX)) {
                     const dflt = this.getPreferenceDefault(key);
                     if (value !== dflt) {
                         changes.push({
@@ -418,27 +390,6 @@ export function BaseSessionModel(_pluginManager) {
         clearPreferenceOverride(key) {
             self.preferencesOverrides.delete(key);
         },
-        /**
-         * #action
-         * revert one row emitted by `getPreferenceChanges`, addressed by its
-         * display `path`. Backs the per-entry reset in the Preferences dialog's
-         * "Reset to defaults" confirmation.
-         *
-         * Lives here rather than in that dialog because this model owns both path
-         * shapes it has to undo: a promoted per-display-type default, whose row
-         * path is a readable label over a flat composite storage key, and every
-         * other override, whose path *is* its key. The dialog used to re-derive
-         * the first case from an exported path-head constant.
-         */
-        resetPreferenceChange(path) {
-            const [head, displayType, slot] = path;
-            if (head === DISPLAY_TYPE_DEFAULTS_PATH_HEAD && displayType && slot) {
-                this.setDisplayTypeDefault(displayType, slot, undefined);
-            }
-            else if (head) {
-                this.clearPreferenceOverride(head);
-            }
-        },
         /**
          * #action
          * set the global scroll-to-zoom preference (see the `scrollZoom` getter)

package/esm/Session/MultipleViews.d.ts

@@ -1660,7 +1660,6 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
     setPreferenceOverride(key: string, value: unknown): void;
     clearPreferenceOverrides(): void;
     clearPreferenceOverride(key: string): void;
-    resetPreferenceChange(path: string[]): void;
     setScrollZoom(flag: boolean): void;
     setDisplayTypeDefault(displayType: string, slot: string, value: unknown): void;
     setName(str: string): void;

package/esm/Session/MultipleViews.js

@@ -1,7 +1,6 @@
-import { applyOrderWithin, localStorageGetBoolean, localStorageSetBoolean, reorderWithin, } from '@jbrowse/core/util';
+import { applyOrderWithin, localStorageGetBoolean, localStorageSetBoolean, reorderWithin, scheduleDetachedDestroy, } from '@jbrowse/core/util';
 import { addDisposer, applyPatch, cast, detach, getMembers, getParent, hasParent, isReferenceType, isStateTreeNode, types, } from '@jbrowse/mobx-state-tree';
 import { autorun } from 'mobx';
-import { scheduleDetachedDestroy } from '../scheduleDetachedDestroy.js';
 import { BaseSessionModel, isBaseSession } from './BaseSession.js';
 import { DrawerWidgetSessionMixin } from './DrawerWidgets.js';
 // Whether `node` IS `view` or lives somewhere under it. A view can CONTAIN

package/esm/Session/Preferences.d.ts

@@ -1641,7 +1641,6 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
     setPreferenceOverride(key: string, value: unknown): void;
     clearPreferenceOverrides(): void;
     clearPreferenceOverride(key: string): void;
-    resetPreferenceChange(path: string[]): void;
     setScrollZoom(flag: boolean): void;
     setDisplayTypeDefault(displayType: string, slot: string, value: unknown): void;
     setName(str: string): void;

package/esm/Session/SessionTracks.d.ts

@@ -1670,7 +1670,6 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
     setPreferenceOverride(key: string, value: unknown): void;
     clearPreferenceOverrides(): void;
     clearPreferenceOverride(key: string): void;
-    resetPreferenceChange(path: string[]): void;
     setScrollZoom(flag: boolean): void;
     setDisplayTypeDefault(displayType: string, slot: string, value: unknown): void;
     setName(str: string): void;
@@ -1702,6 +1701,8 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
 } & {
     getTrackById(id: string): AnyConfigurationModel | undefined;
     getTracksById(): Record<string, AnyConfigurationModel>;
+} & {
+    afterAttach(): void;
 } & {
     addSessionTrackConf(trackConf: AnyConfiguration): any;
     publishTrackConf(trackConf: AnyConfiguration): any;

package/esm/Session/Tracks.d.ts

@@ -1638,7 +1638,6 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
     setPreferenceOverride(key: string, value: unknown): void;
     clearPreferenceOverrides(): void;
     clearPreferenceOverride(key: string): void;
-    resetPreferenceChange(path: string[]): void;
     setScrollZoom(flag: boolean): void;
     setDisplayTypeDefault(displayType: string, slot: string, value: unknown): void;
     setName(str: string): void;
@@ -1691,6 +1690,8 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
      * @deprecated
      */
     getTracksById(): Record<string, AnyConfigurationModel>;
+} & {
+    afterAttach(): void;
 } & {
     /**
      * #action
@@ -1736,10 +1737,6 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
      * session, which is the destination every such caller wanted: a track a
      * plugin stands up for one user is not a catalog entry. Nothing in tree
      * may call it — `no-restricted-syntax` says so.
-     *
-     * Spelled out rather than delegating through `this`, for the reason
-     * `SessionTracks.addToSession` is a plain closure: an action whose return
-     * type is inferred from a sibling's makes the pair circular.
      */
     addTrackConf(trackConf: AnyConfiguration): any;
     /**

package/esm/Session/Tracks.js

@@ -1,6 +1,6 @@
 import { expandLooseTrackConfig } from '@jbrowse/core/util/tracks';
-import { types } from '@jbrowse/mobx-state-tree';
-import { computed } from 'mobx';
+import { addDisposer, types } from '@jbrowse/mobx-state-tree';
+import { autorun, computed } from 'mobx';
 import { BaseSessionModel, isBaseSession } from './BaseSession.js';
 import { isSessionWithConnections } from './Connections.js';
 import { ReferenceManagementSessionMixin } from './ReferenceManagement.js';
@@ -24,16 +24,11 @@ export function TracksManagerSessionMixin(pluginManager) {
         // One index trackId → config for all tracks, assembly sequences, and
         // connection tracks. Frozen jbrowse.tracks entries stay plain objects
         // here; hydration to MST nodes happens lazily in TrackConfigurationReference
-        // on first access. Cached, so the N per-id lookups below share one rebuild
-        // per change rather than each re-scanning.
-        //
-        // `keepAlive` is what makes that last sentence true, and it is load
-        // bearing: an unobserved computed re-derives on EVERY read, and this one
-        // walks every track, assembly and connection the session can resolve. A
-        // reader inside a reaction or an MST action was already fine — MobX
-        // caches within a batch, which is why the resolvers and `showTrackGeneric`
-        // never showed it. Ranking search hits is the caller that is neither, and
-        // it cost 33ms per search on a 2000-track config against 0.07ms held.
+        // on first access. Held hot by the autorun in afterAttach, so a reader
+        // outside any reaction (ranking search hits: 33ms per search unheld on a
+        // 2000-track config, 0.07ms held) gets the cache too. Not `keepAlive`: that
+        // subscription never ends, and it reaches jbrowse.tracks on the root, so
+        // it pinned every superseded session for the tab's life.
         const tracksByIdRecord = computed(() => {
             const temporaryAssemblies = 'temporaryAssemblies' in self
                 ? self.temporaryAssemblies
@@ -59,7 +54,7 @@ export function TracksManagerSessionMixin(pluginManager) {
                     e.config,
                 ]),
             ]);
-        }, { keepAlive: true });
+        }, { name: 'tracksByIdRecord' });
         // Per-id computed cache backing getTrackById. Resolving one track's config
         // subscribes only to that id's computed, so editing track A leaves track
         // B's observers untouched: an unedited id's entry keeps its object identity
@@ -102,24 +97,15 @@ export function TracksManagerSessionMixin(pluginManager) {
         };
     })
         .actions(self => ({
-        /**
-         * #action
-         * Add a track config to *this session*.
-         *
-         * This mixin's session has no separate session-track store, so the
-         * destination is the jbrowse config — which in the products that compose
-         * it (desktop) is the single user's own file rather than something a
-         * server hands other visitors, so the two scopes are the same place.
-         * Defined here anyway so that every session has it: a feature standing a
-         * track up on the user's behalf can then call one action everywhere
-         * instead of asking which mixin it landed on.
-         * `SessionTracksManagerSessionMixin` overrides it with the real
-         * session-scoped store.
-         */
-        addSessionTrackConf(trackConf) {
+        afterAttach() {
+            addDisposer(self, autorun(() => {
+                self.getTracksById();
+            }));
+        },
+    }))
+        .actions(self => {
+        function addToSession(trackConf) {
             assertTrackConfOutlivesItsAssemblies(self, trackConf, 'jbrowse.tracks');
-            // the config's own adder appends without looking, so a re-add under a
-            // known id used to leave two entries with the first one winning
             const expanded = expandLooseTrackConfig(trackConf, pluginManager);
             const { trackId, type } = expanded;
             const existing = self.getTrackById(trackId);
@@ -132,79 +118,93 @@ export function TracksManagerSessionMixin(pluginManager) {
                 return existing;
             }
             return self.jbrowse.addTrackConf(trackConf);
-        },
-        /**
-         * #action
-         * Add a track config wherever *this user's* catalog edits belong — the
-         * "Add track" workflows, where an admin adding a track means to add it
-         * for the whole site. `SessionTracksManagerSessionMixin` overrides it to
-         * send a non-admin's to the session instead; here there is only the one
-         * destination.
-         *
-         * Anything that is not an Add-track workflow wants
-         * `addSessionTrackConf`: a track a feature stands up on the user's behalf
-         * — a search result, a computed consensus, a reconstruction's labels — is
-         * not a catalog entry, and publishing one writes it into the config.json
-         * every visitor is served, once per click.
-         */
-        publishTrackConf(trackConf) {
-            assertTrackConfOutlivesItsAssemblies(self, trackConf, 'jbrowse.tracks');
-            return self.jbrowse.addTrackConf(trackConf);
-        },
-        /**
-         * #action
-         * Deprecated alias of `addSessionTrackConf`. Call that, or
-         * `publishTrackConf`, which say which destination they mean.
-         *
-         * @deprecated
-         *
-         * Kept because a prebuilt plugin bundle reaches this by name at runtime
-         * and cannot be recompiled — `jbrowse-plugin-protein3d` calls it, and a
-         * member lookup that stops resolving throws nothing at all
-         * (`pluginFacingSessionApi.test.ts` is the guard). It now means the
-         * session, which is the destination every such caller wanted: a track a
-         * plugin stands up for one user is not a catalog entry. Nothing in tree
-         * may call it — `no-restricted-syntax` says so.
-         *
-         * Spelled out rather than delegating through `this`, for the reason
-         * `SessionTracks.addToSession` is a plain closure: an action whose return
-         * type is inferred from a sibling's makes the pair circular.
-         */
-        addTrackConf(trackConf) {
-            assertTrackConfOutlivesItsAssemblies(self, trackConf, 'jbrowse.tracks');
-            return self.jbrowse.addTrackConf(trackConf);
-        },
-        /**
-         * #action
-         * Persist edited track config back to the in-memory jbrowse config. The
-         * session-tracks mixin overrides this so a non-admin's edits become a
-         * shareable session-track override instead.
-         */
-        updateTrackConfiguration(trackConf) {
-            // an opened connection track lives in connectionTrackConfigs, not
-            // jbrowse.tracks; persist its edit there (jbrowse.updateTrackConf would
-            // no-op, since the track isn't in the config). Desktop uses this base
-            // mixin, so without this branch a connection-track edit is lost on
-            // reload.
-            if (isSessionWithConnections(self) &&
-                trackConf.trackId in self.connectionTrackConfigs) {
-                self.updateConnectionTrackConfig(trackConf);
-            }
-            else {
-                self.jbrowse.updateTrackConf(trackConf);
-            }
-        },
-        /**
-         * #action
-         */
-        deleteTrackConf(trackConf) {
-            const { trackId } = trackConf;
-            self.dereferenceTrack(trackId, self.getReferring(trackId));
-            if (self.adminMode) {
-                return self.jbrowse.deleteTrackConf(trackConf);
-            }
-        },
-    }));
+        }
+        return {
+            /**
+             * #action
+             * Add a track config to *this session*.
+             *
+             * This mixin's session has no separate session-track store, so the
+             * destination is the jbrowse config — which in the products that compose
+             * it (desktop) is the single user's own file rather than something a
+             * server hands other visitors, so the two scopes are the same place.
+             * Defined here anyway so that every session has it: a feature standing a
+             * track up on the user's behalf can then call one action everywhere
+             * instead of asking which mixin it landed on.
+             * `SessionTracksManagerSessionMixin` overrides it with the real
+             * session-scoped store.
+             */
+            addSessionTrackConf(trackConf) {
+                return addToSession(trackConf);
+            },
+            /**
+             * #action
+             * Add a track config wherever *this user's* catalog edits belong — the
+             * "Add track" workflows, where an admin adding a track means to add it
+             * for the whole site. `SessionTracksManagerSessionMixin` overrides it to
+             * send a non-admin's to the session instead; here there is only the one
+             * destination.
+             *
+             * Anything that is not an Add-track workflow wants
+             * `addSessionTrackConf`: a track a feature stands up on the user's behalf
+             * — a search result, a computed consensus, a reconstruction's labels — is
+             * not a catalog entry, and publishing one writes it into the config.json
+             * every visitor is served, once per click.
+             */
+            publishTrackConf(trackConf) {
+                assertTrackConfOutlivesItsAssemblies(self, trackConf, 'jbrowse.tracks');
+                return self.jbrowse.addTrackConf(trackConf);
+            },
+            /**
+             * #action
+             * Deprecated alias of `addSessionTrackConf`. Call that, or
+             * `publishTrackConf`, which say which destination they mean.
+             *
+             * @deprecated
+             *
+             * Kept because a prebuilt plugin bundle reaches this by name at runtime
+             * and cannot be recompiled — `jbrowse-plugin-protein3d` calls it, and a
+             * member lookup that stops resolving throws nothing at all
+             * (`pluginFacingSessionApi.test.ts` is the guard). It now means the
+             * session, which is the destination every such caller wanted: a track a
+             * plugin stands up for one user is not a catalog entry. Nothing in tree
+             * may call it — `no-restricted-syntax` says so.
+             */
+            addTrackConf(trackConf) {
+                return addToSession(trackConf);
+            },
+            /**
+             * #action
+             * Persist edited track config back to the in-memory jbrowse config. The
+             * session-tracks mixin overrides this so a non-admin's edits become a
+             * shareable session-track override instead.
+             */
+            updateTrackConfiguration(trackConf) {
+                // an opened connection track lives in connectionTrackConfigs, not
+                // jbrowse.tracks; persist its edit there (jbrowse.updateTrackConf would
+                // no-op, since the track isn't in the config). Desktop uses this base
+                // mixin, so without this branch a connection-track edit is lost on
+                // reload.
+                if (isSessionWithConnections(self) &&
+                    trackConf.trackId in self.connectionTrackConfigs) {
+                    self.updateConnectionTrackConfig(trackConf);
+                }
+                else {
+                    self.jbrowse.updateTrackConf(trackConf);
+                }
+            },
+            /**
+             * #action
+             */
+            deleteTrackConf(trackConf) {
+                const { trackId } = trackConf;
+                self.dereferenceTrack(trackId, self.getReferring(trackId));
+                if (self.adminMode) {
+                    return self.jbrowse.deleteTrackConf(trackConf);
+                }
+            },
+        };
+    });
 }
 /** Type guard for SessionWithTracks */
 export function isSessionWithTracks(thing) {

package/esm/index.d.ts

@@ -1,6 +1,6 @@
 export type { AssertExtends, AssertNotAny } from './assertExtends.ts';
 export { asRoot, asSession } from './siblingCast.ts';
-export { scheduleDetachedDestroy } from './scheduleDetachedDestroy.ts';
+export { scheduleDetachedDestroy } from '@jbrowse/core/util';
 export { BaseRootModelFactory, FormatAboutConfigSchemaFactory, FormatDetailsConfigSchemaFactory, HierarchicalConfigSchemaFactory, InternetAccountsRootModelMixin, PreferencesConfigSchemaFactory, createConfigModel, exportSessionMenuItem, importSessionMenuItem, isRootModel, newSessionMenuItem, openConnectionMenuItem, openTrackMenuItem, pluginStoreMenuItem, preferencesMenuItem, redoMenuItem, undoMenuItem, workspacesMenuItem, } from './RootModel/index.ts';
 export type { BaseRootModel, BaseRootModelType, RootConfigurationSnapshot, RootModelWithInternetAccounts, RootModelWithInternetAccountsType, } from './RootModel/index.ts';
 export { BaseSessionModel, ConnectionManagementSessionMixin, DrawerWidgetSessionMixin, MultipleViewsSessionMixin, PreferencesSessionMixin, ReferenceManagementSessionMixin, SessionTracksManagerSessionMixin, ThemeManagerSessionMixin, TrackMenuItemsSessionMixin, TrackMenuSessionMixin, TracksManagerSessionMixin, aboutTrackMenuItem, bakePromotedDefaultsIntoSnapshot, bakeSessionCascades, getShareableSessionSnapshot, copyTrackSnapshot, finalizeSession, isBaseSession, isSession, isSessionWithConnections, isSessionWithDrawerWidgets, isSessionWithMultipleViews, isSessionWithReferenceManagement, isSessionWithThemes, isSessionWithTracks, pluginExtraTrackItems, trackActionItems, trackActionMenuItems, trackListMenuItems, } from './Session/index.ts';

package/esm/index.js

@@ -1,5 +1,5 @@
 export { asRoot, asSession } from './siblingCast.js';
-export { scheduleDetachedDestroy } from './scheduleDetachedDestroy.js';
+export { scheduleDetachedDestroy } from '@jbrowse/core/util';
 export { BaseRootModelFactory, FormatAboutConfigSchemaFactory, FormatDetailsConfigSchemaFactory, HierarchicalConfigSchemaFactory, InternetAccountsRootModelMixin, PreferencesConfigSchemaFactory, createConfigModel, exportSessionMenuItem, importSessionMenuItem, isRootModel, newSessionMenuItem, openConnectionMenuItem, openTrackMenuItem, pluginStoreMenuItem, preferencesMenuItem, redoMenuItem, undoMenuItem, workspacesMenuItem, } from './RootModel/index.js';
 export { BaseSessionModel, ConnectionManagementSessionMixin, DrawerWidgetSessionMixin, MultipleViewsSessionMixin, PreferencesSessionMixin, ReferenceManagementSessionMixin, SessionTracksManagerSessionMixin, ThemeManagerSessionMixin, TrackMenuItemsSessionMixin, TrackMenuSessionMixin, TracksManagerSessionMixin, aboutTrackMenuItem, bakePromotedDefaultsIntoSnapshot, bakeSessionCascades, getShareableSessionSnapshot, copyTrackSnapshot, finalizeSession, isBaseSession, isSession, isSessionWithConnections, isSessionWithDrawerWidgets, isSessionWithMultipleViews, isSessionWithReferenceManagement, isSessionWithThemes, isSessionWithTracks, pluginExtraTrackItems, trackActionItems, trackActionMenuItems, trackListMenuItems, } from './Session/index.js';
 export { AboutDialog, Drawer, DrawerControls, DrawerHeader, DrawerWidget, DrawerWidgetSelector, ModalWidget, ModalWidgetAppBar, PreferencesDialog, WidgetBody, WidgetHeading, drawerGridTemplateColumns, } from './ui/index.js';

package/esm/pruneUnbuildableNodes.js

@@ -12,8 +12,11 @@ const HELD_NODES_KEY = 'heldForMissingPlugins';
 // widen the plugin ABI for nothing.
 function buildableElements(pluginManager, group) {
     return pluginManager.getElementTypesInGroup(group).filter(t => {
-        const { stateModel } = t;
-        return isType(stateModel) && isModelType(stateModel);
+        const element = t;
+        if (element.isStateModelLoaded === false) {
+            return false;
+        }
+        return isType(element.stateModel) && isModelType(element.stateModel);
     });
 }
 // optional/stripDefault/late/snapshotProcessor all report the type they wrap,

package/esm/ui/AboutDialogContents.js

@@ -9,6 +9,7 @@ import { makeStyles } from '@jbrowse/core/util/tss-react';
 import { isStateTreeNode } from '@jbrowse/mobx-state-tree';
 import { observer } from 'mobx-react';
 import AssemblyInfoPanel from './AssemblyInfoPanel.js';
+import DescriptionPanel from './DescriptionPanel.js';
 import FileInfoPanel from './FileInfoPanel.js';
 import HeaderButtons from './HeaderButtons.js';
 import RefNameInfoDialog from './RefNameInfoDialog.js';
@@ -49,7 +50,7 @@ const AboutDialogContents = observer(function AboutDialogContents({ config, sess
         session,
         pluginManager,
     });
-    return (_jsxs("div", { className: classes.content, children: [_jsxs(BaseCard, { title: "Configuration", children: [_jsx(HeaderButtons, { conf: conf, hideUris: hideUris, fromDisplayTypeDefaults: fromDisplayTypeDefaults, setShowRefNames: setShowRefNames }), _jsx(Attributes, { attributes: shown, omit: [...hideFields, 'metadata'], hideUris: hideUris })] }), shown.metadata ? (_jsx(BaseCard, { title: "Metadata", children: _jsx(Attributes, { attributes: shown.metadata, hideUris: hideUris }) })) : null, _jsx(AssemblyInfoPanel, { config: config, session: session, hideUris: hideUris }), _jsx(PluggableComponents, { pluginManager: pluginManager, 
+    return (_jsxs("div", { className: classes.content, children: [_jsxs(BaseCard, { title: "Configuration", children: [_jsx(HeaderButtons, { conf: conf, hideUris: hideUris, fromDisplayTypeDefaults: fromDisplayTypeDefaults, setShowRefNames: setShowRefNames }), _jsx(Attributes, { attributes: shown, omit: [...hideFields, 'metadata'], hideUris: hideUris })] }), shown.metadata ? (_jsx(BaseCard, { title: "Metadata", children: _jsx(Attributes, { attributes: shown.metadata, hideUris: hideUris }) })) : null, _jsx(DescriptionPanel, { config: config, session: session }), _jsx(AssemblyInfoPanel, { config: config, session: session, hideUris: hideUris }), _jsx(PluggableComponents, { pluginManager: pluginManager, 
                 /** #extensionPoint Core-extraAboutPanel | sync | Add extra panels to a track's About dialog */
                 name: "Core-extraAboutPanel", props: { session, config } }), hideUris ? null : _jsx(FileInfoPanel, { config: config, session: session }), showRefNames ? (_jsx(RefNameInfoDialog, { session: session, config: config, onClose: () => {
                     setShowRefNames(false);

package/esm/ui/DescriptionPanel.d.ts

@@ -0,0 +1,3 @@
+import type { AboutPanelProps } from './util.ts';
+declare const DescriptionPanel: ({ config, }: AboutPanelProps) => import("react").JSX.Element | null;
+export default DescriptionPanel;

package/esm/ui/DescriptionPanel.js

@@ -0,0 +1,24 @@
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard';
+import { ErrorBanner, LoadingEllipses, SanitizedHTML } from '@jbrowse/core/ui';
+import { openLocation } from '@jbrowse/core/util/io';
+import { makeStyles } from '@jbrowse/core/util/tss-react';
+import { useFetch } from '@jbrowse/core/util/useFetch';
+import { Link, Typography } from '@mui/material';
+import { observer } from 'mobx-react';
+import { getDescriptionHtmlUrl, rebaseDescriptionHtml, } from './descriptionHtml.js';
+const useStyles = makeStyles()(theme => ({
+    provenance: {
+        marginBottom: theme.spacing(1),
+    },
+}));
+const DescriptionCard = observer(function DescriptionCard({ url, }) {
+    const { classes } = useStyles();
+    const { data: html, error, isLoading, } = useFetch(['trackDescriptionHtml', url], async (_name, url) => rebaseDescriptionHtml(await openLocation({ uri: url, locationType: 'UriLocation' }).readFile('utf8'), url));
+    return (_jsxs(BaseCard, { title: "Description", children: [_jsxs(Typography, { variant: "caption", color: "textSecondary", component: "div", className: classes.provenance, children: ["From the track hub, written for the UCSC Genome Browser \u2014 some display options it describes differ in JBrowse.", ' ', _jsx(Link, { href: url, target: "_blank", rel: "noopener noreferrer", children: "View original" })] }), error ? (_jsx(ErrorBanner, { error: error })) : isLoading || html === undefined ? (_jsx(LoadingEllipses, { message: "Loading description" })) : (_jsx(SanitizedHTML, { html: html }))] }));
+});
+const DescriptionPanel = observer(function DescriptionPanel({ config, }) {
+    const url = getDescriptionHtmlUrl(config);
+    return url ? _jsx(DescriptionCard, { url: url }) : null;
+});
+export default DescriptionPanel;

package/esm/ui/DisplayDefaultsSection.d.ts

@@ -1,33 +1,20 @@
+import type { DisplayDefaultsSession } from './displayDefaultChanges.ts';
 import type PluginManager from '@jbrowse/core/PluginManager';
-export interface DisplayDefaultsSession {
-    getDisplayTypeDefaults: () => {
-        displayType: string;
-        slot: string;
-        value: unknown;
-    }[];
-    setDisplayTypeDefault: (displayType: string, slot: string, value: unknown) => void;
-}
+export type { DisplayDefaultsSession } from './displayDefaultChanges.ts';
 /**
  * The inventory of session-wide display-type defaults: every value the user has
  * pinned from a track menu, what it overrides, and a button to clear one.
  *
  * The pin is easy to set and, until this, hard to find again. A pinned default
  * shows on the track-selector badge of any **open** track it moves — but one
- * affecting nothing currently open, one promoted to a value equal to the slot's
- * base, and one that no longer resolves at all (a stale value the cascade
- * refuses, or a display type whose plugin is gone) appear nowhere. The only
- * place that listed them was the "Reset preferences to defaults" confirmation,
- * which is a destructive dialog to have to open in order to read something.
+ * affecting nothing currently open, and one that no longer resolves at all (a
+ * stale value the cascade refuses, or a display type whose plugin is gone)
+ * appear nowhere. The only place that listed them was the "Reset preferences to
+ * defaults" confirmation, which is a destructive dialog to have to open in
+ * order to read something.
  *
  * The empty state is deliberate rather than rendering nothing: it is the one
  * place the app says the capability exists to someone who has never used it.
- *
- * **The slot keeps its schema name**, while the display type gets its authored
- * one. A slot has no menu label to borrow — which row a setting is offered on is
- * a menu fact and declaring the slot promotable is a schema fact, and nothing
- * joins them (that split is why `promotableSlotsWithoutPin` has to walk a built
- * menu at all). A raw slot name is also what the config editor labels its fields
- * with, so the two surfaces agree.
  */
 declare const DisplayDefaultsSection: ({ session, pluginManager, }: {
     session: DisplayDefaultsSession;