@jbrowse/app-core 4.2.1 → 5.0.0-beta.1

package/esm/JBrowseConfig/index.d.ts

@@ -1,117 +1,179 @@
-import type { PluginDefinition } from '@jbrowse/core/PluginLoader';
 import type PluginManager from '@jbrowse/core/PluginManager';
-import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-export declare function JBrowseConfigF({ pluginManager, assemblyConfigSchema, }: {
+import type { AnyConfigurationSchemaType, ConfigurationSchemaDefinition } from '@jbrowse/core/configuration';
+import type { PluginDefinition } from '@jbrowse/core/pluginDefinitions';
+export { DEFAULT_SHARE_URL } from './RootConfiguration.ts';
+/**
+ * #config JBrowseRootConfig
+ * #category root
+ *
+ * this is a config model representing a config.json (for jbrowse-web) or
+ * somefile.jbrowse (for jbrowse-desktop, where configs have the .jbrowse
+ * extension)
+ *
+ * also includes any pluginManager.pluginConfigurationSchemas(), so plugins
+ * that have a configurationSchema field on their class are mixed into this
+ * object
+ */
+export declare function JBrowseConfigF({ pluginManager, assemblyConfigSchema, extraConfigSlots, }: {
     pluginManager: PluginManager;
     assemblyConfigSchema: AnyConfigurationSchemaType;
-    adminMode?: boolean;
+    extraConfigSlots?: ConfigurationSchemaDefinition;
 }): import("@jbrowse/mobx-state-tree").IModelType<{
     configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        rpc: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-            defaultDriver: {
-                type: string;
-                description: string;
-                defaultValue: string;
+        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;
+            };
+            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;
             };
-            drivers: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ITypeUnion<import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<Record<string, any>>> | undefined, import("@jbrowse/mobx-state-tree").ModelSnapshotType<Record<string, any>>, ({} & Partial<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<Record<string, any>>> & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject) | undefined>>, [undefined]>;
         }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-        highResolutionScaling: {
-            type: string;
-            defaultValue: number;
-        };
-        formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-            feature: {
-                type: string;
-                description: string;
-                defaultValue: {};
-                contextVariable: 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"];
             };
-            subfeatures: {
-                type: string;
-                description: string;
-                defaultValue: {};
-                contextVariable: string[];
+            readonly subfeatures: {
+                readonly type: "frozen";
+                readonly description: "adds extra fields to the subfeatures of a feature";
+                readonly defaultValue: {};
+                readonly contextVariable: ["feature"];
             };
-            depth: {
-                type: string;
-                defaultValue: number;
-                description: string;
+            readonly depth: {
+                readonly type: "maybeNumber";
+                readonly description: "levels of subfeature the formatDetails.subfeatures callback runs on, default 2";
             };
-            maxDepth: {
-                type: string;
-                defaultValue: number;
-                description: string;
+            readonly maxDepth: {
+                readonly type: "maybeNumber";
+                readonly description: "hide subfeatures nested deeper than this, default no limit";
             };
         }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-        formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-            config: {
-                type: string;
-                description: string;
-                defaultValue: {};
-                contextVariable: 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"];
             };
-            hideUris: {
-                type: string;
-                defaultValue: boolean;
+            readonly hideUris: {
+                readonly type: "boolean";
+                readonly defaultValue: false;
             };
         }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-        shareURL: {
-            type: string;
-            defaultValue: string;
+        readonly shareURL: {
+            readonly type: "string";
+            readonly defaultValue: "https://share.jbrowse.org/api/v1/";
+            readonly advanced: true;
         };
-        disableAnalytics: {
-            type: string;
-            defaultValue: boolean;
+        readonly disableAnalytics: {
+            readonly type: "boolean";
+            readonly defaultValue: false;
+            readonly advanced: true;
         };
-        hierarchical: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-            sort: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-                trackNames: {
-                    type: string;
-                    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;
                 };
-                categories: {
-                    type: string;
-                    defaultValue: boolean;
+                readonly categories: {
+                    readonly type: "boolean";
+                    readonly defaultValue: false;
                 };
             }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-            defaultFolderCategories: {
-                type: string;
-                description: string;
-                defaultValue: never[];
+            readonly defaultFolderCategories: {
+                readonly type: "stringArray";
+                readonly description: "list of category names to display as folders by default";
+                readonly defaultValue: readonly [];
             };
-            defaultCollapsed: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-                categoryNames: {
-                    type: string;
-                    defaultValue: never[];
+            readonly defaultCollapsed: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+                readonly categoryNames: {
+                    readonly type: "stringArray";
+                    readonly defaultValue: readonly [];
                 };
-                topLevelCategories: {
-                    type: string;
-                    defaultValue: boolean;
+                readonly topLevelCategories: {
+                    readonly type: "boolean";
+                    readonly defaultValue: false;
                 };
-                subCategories: {
-                    type: string;
-                    defaultValue: boolean;
+                readonly subCategories: {
+                    readonly type: "boolean";
+                    readonly defaultValue: false;
                 };
             }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
         }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-        theme: {
-            type: string;
-            defaultValue: {};
+        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";
+            };
+            readonly scrollZoom: {
+                readonly type: "boolean";
+                readonly defaultValue: false;
+            };
+            readonly numberGrouping: {
+                readonly type: "boolean";
+                readonly defaultValue: true;
+            };
+            readonly useWorkspaces: {
+                readonly type: "boolean";
+                readonly defaultValue: false;
+            };
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+        readonly theme: {
+            readonly type: "frozen";
+            readonly description: "Material UI theme overrides applied to the JBrowse UI";
+            readonly defaultValue: {};
         };
-        extraThemes: {
-            type: string;
-            defaultValue: {};
+        readonly extraThemes: {
+            readonly type: "frozen";
+            readonly description: "additional named themes the user can switch between";
+            readonly defaultValue: {};
+            readonly advanced: true;
         };
-        logoPath: {
-            type: string;
-            defaultValue: {
-                uri: string;
-                locationType: string;
+        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;
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    /**
+     * #slot
+     * defines plugins of the format
+     * ```typescript
+     * type PluginDefinition=
+     *    { umdUrl: string, name:string } |
+     *    { url: string, name: string } |
+     *    { esmUrl: string } |
+     *    { cjsUrl: string } |
+     *    { umdLoc: { uri: string } } |
+     *    { esmLoc: { uri: string } } |
+     * ```
+     */
     plugins: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<PluginDefinition, PluginDefinition, PluginDefinition>>;
+    /**
+     * #slot
+     * configuration of the assemblies in the instance, see BaseAssembly
+     */
     assemblies: import("@jbrowse/mobx-state-tree").IArrayType<AnyConfigurationSchemaType>;
+    /**
+     * #slot
+     * track configuration is an array of track config schemas. multiple
+     * instances of a track can exist that use the same configuration.
+     * Always uses frozen for performance - editing creates temporary MST models.
+     */
     tracks: import("@jbrowse/mobx-state-tree").IType<{
         [key: string]: unknown;
         trackId: string;
@@ -122,9 +184,32 @@ export declare function JBrowseConfigF({ pluginManager, assemblyConfigSchema, }:
         [key: string]: unknown;
         trackId: string;
     }[]>;
-    internetAccounts: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
-    aggregateTextSearchAdapters: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
-    connections: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
+    /**
+     * #slot
+     * configuration for internet accounts, see InternetAccounts
+     */
+    internetAccounts: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
+    /**
+     * #slot
+     * configuration for aggregate text search adapters (created by e.g.
+     * jbrowse text-index, but can be a pluggable TextSearchAdapter type)
+     */
+    aggregateTextSearchAdapters: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
+    /**
+     * #slot
+     * configuration for connections
+     */
+    connections: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
+    /**
+     * #slot
+     * the session loaded when no session is otherwise specified, e.g. the
+     * initial view shown on first load
+     */
     defaultSession: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IType<any, any, any>, [undefined]>;
+    /**
+     * #slot
+     * named sessions bundled with the config that a user can open from the
+     * session selector
+     */
     preConfiguredSessions: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<any, any, any>>;
 }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;

package/esm/JBrowseConfig/index.js

@@ -1,19 +1,79 @@
 import { types } from '@jbrowse/mobx-state-tree';
-import RootConfiguration from "./RootConfiguration.js";
-export function JBrowseConfigF({ pluginManager, assemblyConfigSchema, }) {
+import RootConfiguration from './RootConfiguration.js';
+export { DEFAULT_SHARE_URL } from './RootConfiguration.js';
+/**
+ * #config JBrowseRootConfig
+ * #category root
+ *
+ * this is a config model representing a config.json (for jbrowse-web) or
+ * somefile.jbrowse (for jbrowse-desktop, where configs have the .jbrowse
+ * extension)
+ *
+ * also includes any pluginManager.pluginConfigurationSchemas(), so plugins
+ * that have a configurationSchema field on their class are mixed into this
+ * object
+ */
+export function JBrowseConfigF({ pluginManager, assemblyConfigSchema, extraConfigSlots, }) {
     return types.model('JBrowseConfig', {
         configuration: RootConfiguration({
             pluginManager,
+            extraConfigSlots,
         }),
+        /**
+         * #slot
+         * defines plugins of the format
+         * ```typescript
+         * type PluginDefinition=
+         *    { umdUrl: string, name:string } |
+         *    { url: string, name: string } |
+         *    { esmUrl: string } |
+         *    { cjsUrl: string } |
+         *    { umdLoc: { uri: string } } |
+         *    { esmLoc: { uri: string } } |
+         * ```
+         */
         plugins: types.array(types.frozen()),
+        /**
+         * #slot
+         * configuration of the assemblies in the instance, see BaseAssembly
+         */
         assemblies: types.array(assemblyConfigSchema),
+        /**
+         * #slot
+         * track configuration is an array of track config schemas. multiple
+         * instances of a track can exist that use the same configuration.
+         * Always uses frozen for performance - editing creates temporary MST models.
+         */
         tracks: types.frozen([]),
+        /**
+         * #slot
+         * configuration for internet accounts, see InternetAccounts
+         */
         internetAccounts: types.array(pluginManager.pluggableConfigSchemaType('internet account')),
+        /**
+         * #slot
+         * configuration for aggregate text search adapters (created by e.g.
+         * jbrowse text-index, but can be a pluggable TextSearchAdapter type)
+         */
         aggregateTextSearchAdapters: types.array(pluginManager.pluggableConfigSchemaType('text search adapter')),
+        /**
+         * #slot
+         * configuration for connections
+         */
         connections: types.array(pluginManager.pluggableConfigSchemaType('connection')),
+        /**
+         * #slot
+         * the session loaded when no session is otherwise specified, e.g. the
+         * initial view shown on first load
+         */
         defaultSession: types.optional(types.frozen(), {
             name: 'New Session',
         }),
+        /**
+         * #slot
+         * named sessions bundled with the config that a user can open from the
+         * session selector
+         */
         preConfiguredSessions: types.array(types.frozen()),
         ...pluginManager.pluginConfigurationRootSchemas(),
     });