@jbrowse/product-core 5.0.0-beta.1 → 5.0.0-beta.10

package/esm/RootModel/createConfigModel.d.ts

@@ -5,107 +5,117 @@ import type { IAnyType } from '@jbrowse/mobx-state-tree';
 declare function rootConfigurationSchema(): 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 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 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 theme: {
-        readonly type: "frozen";
-        readonly defaultValue: {};
+        type: "frozen";
+    } & {
+        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>>;
 /**
  * What an embedder may put in `createViewState`'s `configuration` option: every
  * root slot and sub-schema by name, values unchecked. Derived from the schema
@@ -117,116 +127,131 @@ export declare function createConfigModel(pluginManager: PluginManager, assembly
     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 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;
+            };
+            readonly developerMode: {
+                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 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 theme: {
-            readonly type: "frozen";
-            readonly defaultValue: {};
+            type: "frozen";
+        } & {
+            defaultValue: unknown;
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    assembly: IAnyType;
-    tracks: import("@jbrowse/mobx-state-tree").IArrayType<IAnyType>;
-    internetAccounts: import("@jbrowse/mobx-state-tree").IArrayType<IAnyType>;
-    connections: import("@jbrowse/mobx-state-tree").IArrayType<IAnyType>;
-    aggregateTextSearchAdapters: import("@jbrowse/mobx-state-tree").IArrayType<IAnyType>;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+    /**
+     * One genome in the ordinary case, several where the view draws them
+     * together — a circular view's synteny ribbons need both ends of an
+     * alignment on the circle. The order is the order a view lays them out
+     * in.
+     */
+    assemblies: import("@jbrowse/mobx-state-tree").IArrayType<IAnyType>;
+    tracks: import("@jbrowse/mobx-state-tree").IType<Record<string, unknown>[] | null | undefined, Record<string, unknown>[], Record<string, unknown>[]>;
+    internetAccounts: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/PluginManager").PluggableConfigSchemaType>;
+    connections: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/PluginManager").PluggableConfigSchemaType>;
+    aggregateTextSearchAdapters: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/PluginManager").PluggableConfigSchemaType>;
     plugins: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
 }, {
-    readonly assemblies: any[];
-    readonly assemblyName: string;
+    readonly assemblyNames: string[];
     readonly rpcManager: RpcManager;
 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;
 export {};

package/esm/RootModel/createConfigModel.js

@@ -1,5 +1,7 @@
 import { ConfigurationSchema, FormatAboutConfigSchemaFactory, FormatDetailsConfigSchemaFactory, readConfObject, } from '@jbrowse/core/configuration';
+import { migrateRetiredDisplays } from '@jbrowse/core/pluggableElementTypes/models';
 import RpcManager from '@jbrowse/core/rpc/RpcManager';
+import { expandLooseSearchIndex } from '@jbrowse/core/util/expandLooseSearchIndex';
 import { expandLooseTrackConfig } from '@jbrowse/core/util/tracks';
 import { getParent, types } from '@jbrowse/mobx-state-tree';
 import { HierarchicalConfigSchemaFactory } from './HierarchicalConfig.js';
@@ -22,32 +24,51 @@ export function createConfigModel(pluginManager, assemblyConfigSchemasType) {
     return (types
         .model('Configuration', {
         configuration: rootConfigurationSchema(),
-        assembly: assemblyConfigSchemasType,
-        tracks: types.array(pluginManager.pluggableConfigSchemaType('track')),
+        /**
+         * One genome in the ordinary case, several where the view draws them
+         * together — a circular view's synteny ribbons need both ends of an
+         * alignment on the circle. The order is the order a view lays them out
+         * in.
+         */
+        assemblies: types.array(assemblyConfigSchemasType),
+        tracks: types.frozen([]),
         internetAccounts: types.array(pluginManager.pluggableConfigSchemaType('internet account')),
         connections: types.array(pluginManager.pluggableConfigSchemaType('connection')),
         aggregateTextSearchAdapters: types.array(pluginManager.pluggableConfigSchemaType('text search adapter')),
         plugins: types.frozen(),
     })
-        // The one assembly is what every loose `{ trackId, uri }` track is on, so
-        // a snapshot need not repeat its name per track.
+        // The first assembly is what every loose `{ trackId, uri }` track is on,
+        // so a snapshot need not repeat its name per track. `tracks` is frozen,
+        // so a retired display type stays spelt as written until the track
+        // hydrates — and the track selector reads these entries before that, so
+        // they carry the current name here as they do in app-core's JBrowseModel.
         .preProcessSnapshot((snap) => {
-        const tracks = snap?.tracks;
-        const assemblyName = snap?.assembly
-            ?.name;
-        return Array.isArray(tracks)
+        const { tracks, aggregateTextSearchAdapters: indexes } = snap ?? {};
+        const assemblyName = snap?.assemblies?.[0]?.name;
+        return snap
             ? {
                 ...snap,
-                tracks: tracks.map(t => expandLooseTrackConfig(t, pluginManager, assemblyName)),
+                ...(Array.isArray(tracks)
+                    ? {
+                        tracks: tracks.map(t => {
+                            const track = expandLooseTrackConfig(t, pluginManager, assemblyName);
+                            return track && typeof track === 'object'
+                                ? migrateRetiredDisplays(pluginManager, track)
+                                : track;
+                        }),
+                    }
+                    : {}),
+                ...(Array.isArray(indexes)
+                    ? {
+                        aggregateTextSearchAdapters: indexes.map(i => expandLooseSearchIndex(i, assemblyName ? [assemblyName] : undefined)),
+                    }
+                    : {}),
             }
             : snap;
     })
         .views(self => ({
-        get assemblies() {
-            return [self.assembly];
-        },
-        get assemblyName() {
-            return readConfObject(self.assembly, 'name');
+        get assemblyNames() {
+            return self.assemblies.map(a => readConfObject(a, 'name'));
         },
         get rpcManager() {
             return getParent(self).rpcManager;

package/esm/RootModel/menuItems.js

@@ -27,7 +27,7 @@ export function importSessionMenuItem() {
         label: 'Import session...',
         icon: PublishIcon,
         onClick: (session) => {
-            session.showWidget(session.addWidget('ImportSessionWidget', 'importSessionWidget'));
+            session.openWidget('ImportSessionWidget', 'importSessionWidget');
         },
     };
 }
@@ -39,9 +39,9 @@ export function exportSessionMenuItem() {
             const { saveAs } = await import('@jbrowse/core/util/FileSaver');
             saveAs(new Blob([
                 JSON.stringify({
-                    // an exported file is read by someone who doesn't have this
-                    // browser's promoted display-type defaults, so flatten the
-                    // cascade into it (same rule as ShareDialog)
+                    // an exported file is read by someone whose own preferences
+                    // differ, so stamp what the live session resolves at read
+                    // time (same rule as ShareDialog)
                     session: getShareableSessionSnapshot(session),
                 }, null, 2),
             ], { type: 'text/plain;charset=utf-8' }), 'session.json');
@@ -58,10 +58,9 @@ export function openTrackMenuItem() {
                 session.notify('Please open a view to add a track first');
             }
             else {
-                const widget = session.addWidget('AddTrackWidget', 'addTrackWidget', {
+                session.openWidget('AddTrackWidget', 'addTrackWidget', {
                     view: firstView.id,
                 });
-                session.showWidget(widget);
                 if (session.views.length > 1) {
                     session.notify(MULTI_VIEW_WARNING);
                 }
@@ -74,8 +73,7 @@ export function openConnectionMenuItem() {
         label: 'Open connection...',
         icon: Cable,
         onClick: (session) => {
-            const widget = session.addWidget('AddConnectionWidget', 'addConnectionWidget');
-            session.showWidget(widget);
+            session.openWidget('AddConnectionWidget', 'addConnectionWidget');
         },
     };
 }
@@ -84,7 +82,7 @@ export function pluginStoreMenuItem() {
         label: 'Plugin store',
         icon: ExtensionIcon,
         onClick: (session) => {
-            session.showWidget(session.addWidget('PluginStoreWidget', 'pluginStoreWidget'));
+            session.openWidget('PluginStoreWidget', 'pluginStoreWidget');
         },
     };
 }