@jbrowse/app-core 5.0.0-beta.1 → 5.0.0-beta.11

package/esm/JBrowseModel/index.d.ts

@@ -11,133 +11,137 @@ export declare function JBrowseModelF({ pluginManager, assemblyConfigSchema, ext
     configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         readonly rpc: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
             readonly defaultDriver: {
-                readonly type: "string";
-                readonly description: "the RPC driver to run data fetching on: MainThreadRpcDriver or WebWorkerRpcDriver. Leave empty to use the default for this application";
-                readonly defaultValue: "";
-                readonly advanced: true;
+                type: "string";
+            } & {
+                defaultValue: string;
             };
             readonly workerCount: {
-                readonly type: "number";
-                readonly description: "The number of workers to use. If 0 (the default) JBrowse will decide how many workers to use.";
-                readonly defaultValue: 0;
-                readonly advanced: true;
+                type: "number";
+            } & {
+                defaultValue: number;
             };
-        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
         readonly formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
             readonly feature: {
-                readonly type: "frozen";
-                readonly description: "adds extra fields to the feature details";
-                readonly defaultValue: {};
-                readonly contextVariable: ["feature"];
+                type: "frozen";
+            } & {
+                defaultValue: unknown;
             };
             readonly subfeatures: {
-                readonly type: "frozen";
-                readonly description: "adds extra fields to the subfeatures of a feature";
-                readonly defaultValue: {};
-                readonly contextVariable: ["feature"];
+                type: "frozen";
+            } & {
+                defaultValue: unknown;
             };
             readonly depth: {
-                readonly type: "maybeNumber";
-                readonly description: "levels of subfeature the formatDetails.subfeatures callback runs on, default 2";
+                type: "maybeNumber";
             };
             readonly maxDepth: {
-                readonly type: "maybeNumber";
-                readonly description: "hide subfeatures nested deeper than this, default no limit";
+                type: "maybeNumber";
             };
-        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
         readonly formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
             readonly config: {
-                readonly type: "frozen";
-                readonly description: "formats configuration object in about dialog";
-                readonly defaultValue: {};
-                readonly contextVariable: ["config"];
+                type: "frozen";
+            } & {
+                defaultValue: unknown;
             };
             readonly hideUris: {
-                readonly type: "boolean";
-                readonly defaultValue: false;
+                type: "boolean";
+            } & {
+                defaultValue: boolean;
             };
-        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
         readonly shareURL: {
-            readonly type: "string";
-            readonly defaultValue: "https://share.jbrowse.org/api/v1/";
-            readonly advanced: true;
+            type: "string";
+        } & {
+            defaultValue: string;
         };
         readonly disableAnalytics: {
-            readonly type: "boolean";
-            readonly defaultValue: false;
-            readonly advanced: true;
+            type: "boolean";
+        } & {
+            defaultValue: boolean;
         };
         readonly hierarchical: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
             readonly sort: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
                 readonly trackNames: {
-                    readonly type: "boolean";
-                    readonly defaultValue: false;
+                    type: "boolean";
+                } & {
+                    defaultValue: boolean;
                 };
                 readonly categories: {
-                    readonly type: "boolean";
-                    readonly defaultValue: false;
+                    type: "boolean";
+                } & {
+                    defaultValue: boolean;
                 };
-            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
             readonly defaultFolderCategories: {
-                readonly type: "stringArray";
-                readonly description: "list of category names to display as folders by default";
-                readonly defaultValue: readonly [];
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
             };
             readonly defaultCollapsed: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
                 readonly categoryNames: {
-                    readonly type: "stringArray";
-                    readonly defaultValue: readonly [];
+                    type: "stringArray";
+                } & {
+                    defaultValue: unknown;
                 };
                 readonly topLevelCategories: {
-                    readonly type: "boolean";
-                    readonly defaultValue: false;
+                    type: "boolean";
+                } & {
+                    defaultValue: boolean;
                 };
                 readonly subCategories: {
-                    readonly type: "boolean";
-                    readonly defaultValue: false;
+                    type: "boolean";
+                } & {
+                    defaultValue: boolean;
                 };
-            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
         readonly preferences: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
             readonly animationMode: {
-                readonly model: import("@jbrowse/mobx-state-tree").ISimpleType<"disabled" | "enabled" | "system">;
-                readonly type: "stringEnum";
-                readonly defaultValue: "enabled";
+                type: "stringEnum";
+            } & {
+                model: import("@jbrowse/mobx-state-tree").ISimpleType<"disabled" | "enabled" | "system">;
+            } & {
+                defaultValue: string;
             };
             readonly scrollZoom: {
-                readonly type: "boolean";
-                readonly defaultValue: false;
+                type: "boolean";
+            } & {
+                defaultValue: boolean;
             };
             readonly numberGrouping: {
-                readonly type: "boolean";
-                readonly defaultValue: true;
+                type: "boolean";
+            } & {
+                defaultValue: boolean;
             };
             readonly useWorkspaces: {
-                readonly type: "boolean";
-                readonly defaultValue: false;
+                type: "boolean";
+            } & {
+                defaultValue: boolean;
             };
-        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+            readonly developerMode: {
+                type: "boolean";
+            } & {
+                defaultValue: boolean;
+            };
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
         readonly theme: {
-            readonly type: "frozen";
-            readonly description: "Material UI theme overrides applied to the JBrowse UI";
-            readonly defaultValue: {};
+            type: "frozen";
+        } & {
+            defaultValue: unknown;
         };
         readonly extraThemes: {
-            readonly type: "frozen";
-            readonly description: "additional named themes the user can switch between";
-            readonly defaultValue: {};
-            readonly advanced: true;
+            type: "frozen";
+        } & {
+            defaultValue: unknown;
         };
         readonly logoPath: {
-            readonly type: "fileLocation";
-            readonly description: "path to a custom logo image displayed in the app header";
-            readonly defaultValue: {
-                readonly uri: "";
-                readonly locationType: "UriLocation";
-            };
-            readonly advanced: true;
+            type: "fileLocation";
+        } & {
+            defaultValue: unknown;
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
     plugins: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<PluginDefinition, PluginDefinition, PluginDefinition>>;
     assemblies: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
     tracks: import("@jbrowse/mobx-state-tree").IType<{
@@ -150,9 +154,9 @@ export declare function JBrowseModelF({ pluginManager, assemblyConfigSchema, ext
         [key: string]: unknown;
         trackId: string;
     }[]>;
-    internetAccounts: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
-    aggregateTextSearchAdapters: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
-    connections: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
+    internetAccounts: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/PluginManager").PluggableConfigSchemaType>;
+    aggregateTextSearchAdapters: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/PluginManager").PluggableConfigSchemaType>;
+    connections: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/PluginManager").PluggableConfigSchemaType>;
     defaultSession: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IType<any, any, any>, [undefined]>;
     preConfiguredSessions: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<any, any, any>>;
 }, {
@@ -168,10 +172,7 @@ export declare function JBrowseModelF({ pluginManager, assemblyConfigSchema, ext
     /**
      * #action
      */
-    addAssemblyConf(conf: AnyConfigurationModel): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
-        setSubschema(slotName: string, data: Record<string, unknown>): any;
-        setSlot(slotName: string, value: unknown): void;
-    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | undefined;
+    addAssemblyConf(conf: AnyConfigurationModel): (import("@jbrowse/core/configuration").ConfigNodeProps<any> & import("@jbrowse/core/configuration").ConfigNodeActions & import("@jbrowse/core/configuration").ConfigNodeBrand<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | undefined;
     /**
      * #action
      */
@@ -193,7 +194,7 @@ export declare function JBrowseModelF({ pluginManager, assemblyConfigSchema, ext
      * the array coerces — since callers hand it plain JSON (a session spec's
      * `sessionConnections`, the CLI's add-connection output).
      */
-    addConnectionConf(connectionConf: AnyConfiguration): any;
+    addConnectionConf(connectionConf: AnyConfiguration): (import("@jbrowse/core/configuration").PluggableConfigNode & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/PluginManager").PluggableConfigSchemaType>) | undefined;
     /**
      * #action
      */
@@ -207,7 +208,8 @@ export declare function JBrowseModelF({ pluginManager, assemblyConfigSchema, ext
     /**
      * #action
      * Updates an existing track configuration. Used to sync editable configs
-     * back to the frozen tracks array.
+     * back to the frozen tracks array. A trackId the array repeats replaces
+     * its last entry, the one the session resolves it to.
      */
     updateTrackConf(trackConf: {
         trackId: string;
@@ -219,26 +221,21 @@ export declare function JBrowseModelF({ pluginManager, assemblyConfigSchema, ext
     addPlugin(pluginDefinition: PluginDefinition): void;
     /**
      * #action
-     * Removes the entry that loads from the same url — the version-pinned
-     * definition, not every entry sharing a name, so the update flow's
-     * remove-then-add swaps one version for another.
-     *
-     * A definition naming no loader matches nothing (`isPluginUrl`) rather than
-     * every other url-less entry: `pluginUrl`'s miss value is the display string
-     * 'unknown url', so removing one hand-written broken entry used to filter out
-     * all of them. Such an entry has no InstalledPlugin row to remove it from
-     * either — it never loads, so it is never in `runtimePluginDefinitions` — so
-     * matching nothing costs nothing the UI could reach.
+     * Removes the entry the loaded copy came from — the version-pinned
+     * definition, or the bare store ref that resolved to it. Not every entry
+     * sharing a name or a ref, so the update flow's remove-then-add swaps one
+     * version for another; `holdsPluginVersion` argues both halves.
      */
     removePlugin(pluginDefinition: PluginDefinition): void;
     /**
      * #action
+     * takes the live session or a plain session snapshot
      */
     setDefaultSessionConf(sessionConf: AnyConfigurationModel): void;
     /**
      * #action
      */
-    addInternetAccountConf(internetAccountConf: AnyConfigurationModel): any;
+    addInternetAccountConf(internetAccountConf: AnyConfigurationModel): (import("@jbrowse/core/configuration").PluggableConfigNode & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/PluginManager").PluggableConfigSchemaType>) | undefined;
     /**
      * #action
      */

package/esm/JBrowseModel/index.js

@@ -1,8 +1,9 @@
 import { readConfObject } from '@jbrowse/core/configuration';
-import { isPluginUrl, maybePluginUrl } from '@jbrowse/core/pluginDefinitions';
+import { migrateRetiredDisplays } from '@jbrowse/core/pluggableElementTypes/models';
+import { holdsPluginVersion } from '@jbrowse/core/pluginDefinitions';
+import { expandLooseSearchIndex } from '@jbrowse/core/util/expandLooseSearchIndex';
 import { expandLooseTrackConfig } from '@jbrowse/core/util/tracks';
-import { cast, getParent, getSnapshot, types } from '@jbrowse/mobx-state-tree';
-import { migrateConfigSnapshot } from '@jbrowse/product-core';
+import { cast, getParent, getSnapshot, isStateTreeNode, types, } from '@jbrowse/mobx-state-tree';
 import { toJS } from 'mobx';
 import { JBrowseConfigF } from '../JBrowseConfig/index.js';
 /**
@@ -12,21 +13,34 @@ import { JBrowseConfigF } from '../JBrowseConfig/index.js';
  * config models are MST trees themselves, which is why this state model is
  * allowed to build on one. Generally found on a property named rootModel.jbrowse
  */
-// A config with exactly one assembly is what every loose track is on, so
-// `assemblyNames` may be left off; with several, the track has to say.
+// A config with exactly one assembly is what every loose track and search index
+// is on, so `assemblyNames` may be left off; with several, each has to say.
 function expandLooseTracks(snapshot, pluginManager) {
-    const tracks = snapshot.tracks;
-    if (!Array.isArray(tracks)) {
-        return snapshot;
-    }
-    const assemblies = snapshot.assemblies;
+    const { tracks, assemblies, aggregateTextSearchAdapters: indexes } = snapshot;
     const only = Array.isArray(assemblies) && assemblies.length === 1
         ? assemblies[0].name
         : undefined;
-    const expanded = tracks.map(t => expandLooseTrackConfig(t, pluginManager, only));
-    return expanded.every((t, i) => t === tracks[i])
+    const expandedTracks = Array.isArray(tracks)
+        ? tracks.map(t => {
+            const track = expandLooseTrackConfig(t, pluginManager, only);
+            return track && typeof track === 'object'
+                ? migrateRetiredDisplays(pluginManager, track)
+                : track;
+        })
+        : tracks;
+    const expandedIndexes = Array.isArray(indexes)
+        ? indexes.map(i => expandLooseSearchIndex(i, only ? [only] : undefined))
+        : indexes;
+    const same = (a, b) => !Array.isArray(a) || a.every((x, i) => x === b[i]);
+    return same(expandedTracks, tracks) && same(expandedIndexes, indexes)
         ? snapshot
-        : { ...snapshot, tracks: expanded };
+        : {
+            ...snapshot,
+            ...(expandedTracks ? { tracks: expandedTracks } : {}),
+            ...(expandedIndexes
+                ? { aggregateTextSearchAdapters: expandedIndexes }
+                : {}),
+        };
 }
 export function JBrowseModelF({ pluginManager, assemblyConfigSchema, extraConfigSlots, }) {
     const model = JBrowseConfigF({
@@ -57,17 +71,10 @@ export function JBrowseModelF({ pluginManager, assemblyConfigSchema, extraConfig
             if (!name) {
                 throw new Error('Can\'t add assembly with no "name"');
             }
-            if (self.assemblyNames.includes(name)) {
+            if (self.assemblies.some(a => a.name === name || a.aliases.includes(name))) {
                 throw new Error(`Can't add assembly with name "${name}", an assembly with that name already exists`);
             }
-            const length = self.assemblies.push({
-                ...conf,
-                sequence: {
-                    type: 'ReferenceSequenceTrack',
-                    trackId: `${name}-${Date.now()}`,
-                    ...conf.sequence,
-                },
-            });
+            const length = self.assemblies.push(conf);
             return self.assemblies[length - 1];
         },
         /**
@@ -126,11 +133,12 @@ export function JBrowseModelF({ pluginManager, assemblyConfigSchema, extraConfig
         /**
          * #action
          * Updates an existing track configuration. Used to sync editable configs
-         * back to the frozen tracks array.
+         * back to the frozen tracks array. A trackId the array repeats replaces
+         * its last entry, the one the session resolves it to.
          */
         updateTrackConf(trackConf) {
             const { trackId } = trackConf;
-            const idx = self.tracks.findIndex(t => t.trackId === trackId);
+            const idx = self.tracks.findLastIndex(t => t.trackId === trackId);
             if (idx !== -1) {
                 const newTracks = [...self.tracks];
                 newTracks[idx] = trackConf;
@@ -146,27 +154,21 @@ export function JBrowseModelF({ pluginManager, assemblyConfigSchema, extraConfig
         },
         /**
          * #action
-         * Removes the entry that loads from the same url — the version-pinned
-         * definition, not every entry sharing a name, so the update flow's
-         * remove-then-add swaps one version for another.
-         *
-         * A definition naming no loader matches nothing (`isPluginUrl`) rather than
-         * every other url-less entry: `pluginUrl`'s miss value is the display string
-         * 'unknown url', so removing one hand-written broken entry used to filter out
-         * all of them. Such an entry has no InstalledPlugin row to remove it from
-         * either — it never loads, so it is never in `runtimePluginDefinitions` — so
-         * matching nothing costs nothing the UI could reach.
+         * Removes the entry the loaded copy came from — the version-pinned
+         * definition, or the bare store ref that resolved to it. Not every entry
+         * sharing a name or a ref, so the update flow's remove-then-add swaps one
+         * version for another; `holdsPluginVersion` argues both halves.
          */
         removePlugin(pluginDefinition) {
-            const targetUrl = maybePluginUrl(pluginDefinition);
-            self.plugins = cast(self.plugins.filter(plugin => !isPluginUrl(plugin, targetUrl)));
+            self.plugins = cast(self.plugins.filter(plugin => !holdsPluginVersion(plugin, pluginDefinition)));
             getParent(self).setPluginsUpdated();
         },
         /**
          * #action
+         * takes the live session or a plain session snapshot
          */
         setDefaultSessionConf(sessionConf) {
-            const newDefault = getParent(self).session?.name === sessionConf.name
+            const newDefault = isStateTreeNode(sessionConf)
                 ? getSnapshot(sessionConf)
                 : toJS(sessionConf);
             if (!newDefault.name) {
@@ -195,14 +197,12 @@ export function JBrowseModelF({ pluginManager, assemblyConfigSchema, extraConfig
             return elt ? self.internetAccounts.remove(elt) : false;
         },
     }));
-    // Migrate legacy display types (e.g. LinearPileupDisplay →
-    // LinearAlignmentsDisplay) when ingesting config snapshots so saved
-    // configs from older JBrowse versions still load. `tracks` stays frozen
-    // (ADR-032), so the loose `{ trackId, uri }` form is expanded here, where
-    // the track selector and the trackId index read it, and never by a schema.
+    // `tracks` stays frozen (ADR-032), so the loose `{ trackId, uri }` form is
+    // expanded and a retired display type loaded as its successor here, where
+    // the track selector and the trackId index read them, and never by a schema.
     return types.snapshotProcessor(model, {
         preProcessor(snapshot) {
-            return migrateConfigSnapshot(expandLooseTracks(snapshot, pluginManager));
+            return expandLooseTracks(snapshot, pluginManager);
         },
     });
 }

package/esm/JbApi/index.d.ts

@@ -0,0 +1,2 @@
+export { createJbApi, ensureReExports, safeJson, sessionOf, undeliveredNotifications, waitReady, } from './jbApi.ts';
+export type { JbApi } from './jbApi.ts';

package/esm/JbApi/index.js

@@ -0,0 +1 @@
+export { createJbApi, ensureReExports, safeJson, sessionOf, undeliveredNotifications, waitReady, } from './jbApi.js';