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

package/esm/JBrowseConfig/RootConfiguration.d.ts

@@ -1,6 +1,5 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { ConfigurationSchemaDefinition } from '@jbrowse/core/configuration';
-export declare const DEFAULT_SHARE_URL = "https://share.jbrowse.org/api/v1/";
 /**
  * #config JBrowseConfiguration
  * #category root
@@ -18,183 +17,136 @@ export default function RootConfiguration({ pluginManager, extraConfigSlots, }:
     pluginManager: PluginManager;
     extraConfigSlots?: ConfigurationSchemaDefinition;
 }): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #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;
+            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>>;
-    /**
-     * #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.
-     */
+    }, 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>>;
-    /**
-     * #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.
-     */
+    }, 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>>;
-    /**
-     * #slot configuration.shareURL
-     * URL of the session-sharing backend used by the Share button, a
-     * JBrowse-hosted service by default
-     */
+    }, 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;
     };
-    /**
-     * #slot configuration.disableAnalytics
-     * disables collection of anonymous usage analytics
-     */
     readonly disableAnalytics: {
-        readonly type: "boolean";
-        readonly defaultValue: false;
-        readonly advanced: true;
+        type: "boolean";
+    } & {
+        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;
+                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>>;
-    /**
-     * #slot configuration.preferences
-     * user preferences such as scroll-to-zoom and animation behavior, see
-     * PreferencesConfigSchema
-     */
+        }, 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>>;
-    /**
-     * #slot configuration.theme
-     */
+    }, 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;
     };
-    /**
-     * #slot configuration.extraThemes
-     */
     readonly extraThemes: {
-        readonly type: "frozen";
-        readonly description: "additional named themes the user can switch between";
-        readonly defaultValue: {};
-        readonly advanced: true;
+        type: "frozen";
+    } & {
+        defaultValue: unknown;
     };
-    /**
-     * #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;
+        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>>>;

package/esm/JBrowseConfig/RootConfiguration.js

@@ -1,11 +1,7 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import RpcManager from '@jbrowse/core/rpc/RpcManager';
 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/';
+import { DEFAULT_SHARE_URL } from './defaultShareUrl.js';
 /**
  * #config JBrowseConfiguration
  * #category root
@@ -31,17 +27,15 @@ export default function RootConfiguration({ pluginManager, extraConfigSlots = {}
         /**
          * #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.
+         * panel of every track at once. 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.
+         * every track at once. A track can set the same ones on its own
+         * `formatAbout` and override individual keys.
          */
         formatAbout: FormatAboutConfigSchemaFactory(),
         /**

package/esm/JBrowseConfig/defaultShareUrl.d.ts

@@ -0,0 +1 @@
+export declare const DEFAULT_SHARE_URL = "https://share.jbrowse.org/api/v1/";

package/esm/JBrowseConfig/defaultShareUrl.js

@@ -0,0 +1,5 @@
+// The JBrowse-hosted session-sharing backend. Single source of truth for both
+// the write path (the root config's `shareURL` 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/';

package/esm/JBrowseConfig/index.d.ts

@@ -1,7 +1,7 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { AnyConfigurationSchemaType, ConfigurationSchemaDefinition } from '@jbrowse/core/configuration';
 import type { PluginDefinition } from '@jbrowse/core/pluginDefinitions';
-export { DEFAULT_SHARE_URL } from './RootConfiguration.ts';
+export { DEFAULT_SHARE_URL } from './defaultShareUrl.ts';
 /**
  * #config JBrowseRootConfig
  * #category root
@@ -22,137 +22,137 @@ export declare function JBrowseConfigF({ pluginManager, assemblyConfigSchema, ex
     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>>>;
     /**
      * #slot
      * defines plugins of the format

package/esm/JBrowseConfig/index.js

@@ -1,6 +1,6 @@
 import { types } from '@jbrowse/mobx-state-tree';
 import RootConfiguration from './RootConfiguration.js';
-export { DEFAULT_SHARE_URL } from './RootConfiguration.js';
+export { DEFAULT_SHARE_URL } from './defaultShareUrl.js';
 /**
  * #config JBrowseRootConfig
  * #category root