@jbrowse/app-core 5.0.0-beta.7 → 5.0.0-beta.9

package/esm/JBrowseModel/index.d.ts

@@ -11,137 +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>>>;
         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>>>;
         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>>>;
         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>>>;
             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>>>;
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
         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;
             };
             readonly developerMode: {
-                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>>>;
         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>>>;
     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<{
@@ -172,10 +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
      */

package/esm/JBrowseModel/index.js

@@ -1,5 +1,6 @@
 import { readConfObject } from '@jbrowse/core/configuration';
 import { isPluginUrl, maybePluginUrl } 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';
@@ -12,21 +13,29 @@ 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 => expandLooseTrackConfig(t, pluginManager, only))
+        : 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({