@jbrowse/app-core 4.3.0 → 5.0.0-beta.2

package/esm/JBrowseConfig/RootConfiguration.d.ts

@@ -1,107 +1,200 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
-export default function RootConfiguration({ pluginManager, }: {
+import type { ConfigurationSchemaDefinition } from '@jbrowse/core/configuration';
+export declare const DEFAULT_SHARE_URL = "https://share.jbrowse.org/api/v1/";
+/**
+ * #config JBrowseConfiguration
+ * #category root
+ * this is the entry under the `configuration` key
+ * e.g.
+ * ```json
+ * {
+ *   assemblies,
+ *   tracks,
+ *   configuration: { these entries here  }
+ * }
+ * ```
+ */
+export default function RootConfiguration({ pluginManager, extraConfigSlots, }: {
     pluginManager: PluginManager;
+    extraConfigSlots?: ConfigurationSchemaDefinition;
 }): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    rpc: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        defaultDriver: {
-            type: string;
-            description: string;
-            defaultValue: string;
+    /**
+     * #slot configuration.rpc
+     * configuration for the RPC system that runs data adapters in web workers,
+     * see RpcOptions
+     */
+    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[];
+    /**
+     * #slot configuration.formatDetails
+     * jexl callbacks that add, rewrite or hide fields in the feature-details
+     * panel of every track at once. Four slots, listed at
+     * [FormatDetails](/docs/config/formatdetails); a track can set the same
+     * ones on its own `formatDetails` and override individual keys.
+     */
+    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[];
+    /**
+     * #slot configuration.formatAbout
+     * jexl callbacks that add, rewrite or hide fields in the About dialog of
+     * every track at once. Two slots, listed at
+     * [FormatAbout](/docs/config/formatabout); a track can set the same ones on
+     * its own `formatAbout` and override individual keys.
+     */
+    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;
+    /**
+     * #slot configuration.shareURL
+     * URL of the session-sharing backend used by the Share button, a
+     * JBrowse-hosted service by default
+     */
+    readonly shareURL: {
+        readonly type: "string";
+        readonly defaultValue: "https://share.jbrowse.org/api/v1/";
+        readonly advanced: true;
     };
-    disableAnalytics: {
-        type: string;
-        defaultValue: boolean;
+    /**
+     * #slot configuration.disableAnalytics
+     * disables collection of anonymous usage analytics
+     */
+    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;
+    /**
+     * #slot configuration.hierarchical
+     * configuration for the hierarchical track selector, controlling sorting
+     * and default categories, see HierarchicalConfigSchema
+     */
+    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: {};
+    /**
+     * #slot configuration.preferences
+     * user preferences such as scroll-to-zoom and animation behavior, see
+     * PreferencesConfigSchema
+     */
+    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;
+        };
+        readonly developerMode: {
+            readonly type: "boolean";
+            readonly defaultValue: false;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    /**
+     * #slot configuration.theme
+     */
+    readonly theme: {
+        readonly type: "frozen";
+        readonly description: "Material UI theme overrides applied to the JBrowse UI";
+        readonly defaultValue: {};
     };
-    extraThemes: {
-        type: string;
-        defaultValue: {};
+    /**
+     * #slot configuration.extraThemes
+     */
+    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;
+    /**
+     * #slot configuration.logoPath
+     */
+    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>>;

package/esm/JBrowseConfig/RootConfiguration.js

@@ -1,40 +1,118 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import RpcManager from '@jbrowse/core/rpc/RpcManager';
-import { FormatAboutConfigSchemaFactory, FormatDetailsConfigSchemaFactory, HierarchicalConfigSchemaFactory, } from '@jbrowse/product-core';
-export default function RootConfiguration({ pluginManager, }) {
+import { FormatAboutConfigSchemaFactory, FormatDetailsConfigSchemaFactory, HierarchicalConfigSchemaFactory, PreferencesConfigSchemaFactory, } from '@jbrowse/product-core';
+// The JBrowse-hosted session-sharing backend. Single source of truth for both
+// the write path (this slot's default, read via getConf) and the SessionLoader
+// read path (which reads the raw config snapshot before config is initialized),
+// so the two can't drift onto different endpoints.
+export const DEFAULT_SHARE_URL = 'https://share.jbrowse.org/api/v1/';
+/**
+ * #config JBrowseConfiguration
+ * #category root
+ * this is the entry under the `configuration` key
+ * e.g.
+ * ```json
+ * {
+ *   assemblies,
+ *   tracks,
+ *   configuration: { these entries here  }
+ * }
+ * ```
+ */
+export default function RootConfiguration({ pluginManager, extraConfigSlots = {}, }) {
     return ConfigurationSchema('Root', {
+        ...extraConfigSlots,
+        /**
+         * #slot configuration.rpc
+         * configuration for the RPC system that runs data adapters in web workers,
+         * see RpcOptions
+         */
         rpc: RpcManager.configSchema,
-        highResolutionScaling: {
-            type: 'number',
-            defaultValue: 2,
-        },
+        /**
+         * #slot configuration.formatDetails
+         * jexl callbacks that add, rewrite or hide fields in the feature-details
+         * panel of every track at once. Four slots, listed at
+         * [FormatDetails](/docs/config/formatdetails); a track can set the same
+         * ones on its own `formatDetails` and override individual keys.
+         */
         formatDetails: FormatDetailsConfigSchemaFactory(),
+        /**
+         * #slot configuration.formatAbout
+         * jexl callbacks that add, rewrite or hide fields in the About dialog of
+         * every track at once. Two slots, listed at
+         * [FormatAbout](/docs/config/formatabout); a track can set the same ones on
+         * its own `formatAbout` and override individual keys.
+         */
         formatAbout: FormatAboutConfigSchemaFactory(),
+        /**
+         * #slot configuration.shareURL
+         * URL of the session-sharing backend used by the Share button, a
+         * JBrowse-hosted service by default
+         */
         shareURL: {
             type: 'string',
-            defaultValue: 'https://share.jbrowse.org/api/v1/',
+            defaultValue: DEFAULT_SHARE_URL,
+            advanced: true,
         },
+        /**
+         * #slot configuration.disableAnalytics
+         * disables collection of anonymous usage analytics
+         */
         disableAnalytics: {
             type: 'boolean',
             defaultValue: false,
+            advanced: true,
         },
+        /**
+         * #slot configuration.hierarchical
+         * configuration for the hierarchical track selector, controlling sorting
+         * and default categories, see HierarchicalConfigSchema
+         */
         hierarchical: HierarchicalConfigSchemaFactory(),
+        /**
+         * #slot configuration.preferences
+         * user preferences such as scroll-to-zoom and animation behavior, see
+         * PreferencesConfigSchema
+         */
+        preferences: PreferencesConfigSchemaFactory(),
+        /**
+         * #slot configuration.theme
+         */
         theme: {
             type: 'frozen',
+            description: 'Material UI theme overrides applied to the JBrowse UI',
             defaultValue: {},
         },
+        /**
+         * #slot configuration.extraThemes
+         */
         extraThemes: {
             type: 'frozen',
+            description: 'additional named themes the user can switch between',
             defaultValue: {},
+            advanced: true,
         },
+        /**
+         * #slot configuration.logoPath
+         */
         logoPath: {
             type: 'fileLocation',
+            description: 'path to a custom logo image displayed in the app header',
             defaultValue: {
                 uri: '',
                 locationType: 'UriLocation',
             },
+            advanced: true,
         },
+        /**
+         * #slotAnnot
+         * this is a collection of 'namespaced' configs e.g. configuration.YourPlugin.slot
+         */
         ...pluginManager.pluginConfigurationNamespacedSchemas(),
+        /**
+         * #slotAnnot
+         * this is a collection of 'unnamespaced' configs e.g. configuration.slot
+         */
         ...pluginManager.pluginConfigurationUnnamespacedSchemas(),
     });
 }