@jbrowse/product-core 3.7.0 → 4.0.0

package/esm/Session/Connections.d.ts

@@ -1,158 +1,21 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import type { BaseConnectionConfigModel } from '@jbrowse/core/pluggableElementTypes/models/baseConnectionConfig';
-import type { IAnyStateTreeNode, Instance } from 'mobx-state-tree';
-export declare function ConnectionManagementSessionMixin(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
-    connectionInstances: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
-        name: import("mobx-state-tree").ISimpleType<string>;
-        tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
-        configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-            name: {
-                type: string;
-                defaultValue: string;
-                description: string;
-            };
-            assemblyNames: {
-                type: string;
-                defaultValue: never[];
-                description: string;
-            };
-        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
-    }, {
-        connect(_arg: AnyConfigurationModel): void;
-    } & {
-        afterAttach(): void;
-        addTrackConf(trackConf: ({
-            [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                    [x: string]: any;
-                } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-            } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | Record<string, unknown>): any;
-        addTrackConfs(trackConfs: (({
-            [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                    [x: string]: any;
-                } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-            } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | Record<string, unknown>)[]): void;
-        setTrackConfs(trackConfs: AnyConfigurationModel[]): void;
-        clear(): void;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+import type { IAnyStateTreeNode, Instance } from '@jbrowse/mobx-state-tree';
+export declare function ConnectionManagementSessionMixin(pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<{
+    connectionInstances: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
 }, {
     readonly connections: BaseConnectionConfigModel[];
 } & {
-    makeConnection(configuration: AnyConfigurationModel, initialSnapshot?: {}): ({
-        name: string;
-        tracks: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyModelType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>>;
-        configuration: {
-            [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                    [x: string]: any;
-                } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-            } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-            name: {
-                type: string;
-                defaultValue: string;
-                description: string;
-            };
-            assemblyNames: {
-                type: string;
-                defaultValue: never[];
-                description: string;
-            };
-        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>>;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        connect(_arg: AnyConfigurationModel): void;
-    } & {
-        afterAttach(): void;
-        addTrackConf(trackConf: ({
-            [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                    [x: string]: any;
-                } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-            } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | Record<string, unknown>): any;
-        addTrackConfs(trackConfs: (({
-            [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                    [x: string]: any;
-                } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-            } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | Record<string, unknown>)[]): void;
-        setTrackConfs(trackConfs: AnyConfigurationModel[]): void;
-        clear(): void;
-    } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-        name: import("mobx-state-tree").ISimpleType<string>;
-        tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
-        configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-            name: {
-                type: string;
-                defaultValue: string;
-                description: string;
-            };
-            assemblyNames: {
-                type: string;
-                defaultValue: never[];
-                description: string;
-            };
-        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
-    }, {
-        connect(_arg: AnyConfigurationModel): void;
-    } & {
-        afterAttach(): void;
-        addTrackConf(trackConf: ({
-            [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                    [x: string]: any;
-                } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-            } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | Record<string, unknown>): any;
-        addTrackConfs(trackConfs: (({
-            [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                    [x: string]: any;
-                } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-            } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | Record<string, unknown>)[]): void;
-        setTrackConfs(trackConfs: AnyConfigurationModel[]): void;
-        clear(): void;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
+    makeConnection(configuration: AnyConfigurationModel, initialSnapshot?: {}): any;
     prepareToBreakConnection(configuration: AnyConfigurationModel): (Record<string, number> | (() => void))[] | undefined;
     breakConnection(configuration: AnyConfigurationModel): void;
     deleteConnection(configuration: AnyConfigurationModel): any;
     addConnectionConf(connectionConf: AnyConfigurationModel): any;
     clearConnections(): void;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+    connectionInstances: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
+}>>;
 export type SessionWithConnectionsType = ReturnType<typeof ConnectionManagementSessionMixin>;
 export type SessionWithConnections = Instance<SessionWithConnectionsType>;
 export declare function isSessionWithConnections(session: IAnyStateTreeNode): session is SessionWithConnections;

package/esm/Session/Connections.js

@@ -1,6 +1,6 @@
 import { readConfObject } from '@jbrowse/core/configuration';
-import { types } from 'mobx-state-tree';
-import { isBaseSession } from './BaseSession';
+import { types } from '@jbrowse/mobx-state-tree';
+import { isBaseSession } from "./BaseSession.js";
 export function ConnectionManagementSessionMixin(pluginManager) {
     return types
         .model({
@@ -73,7 +73,17 @@ export function ConnectionManagementSessionMixin(pluginManager) {
         clearConnections() {
             self.connectionInstances.clear();
         },
-    }));
+    }))
+        .postProcessSnapshot(snap => {
+        if (!snap) {
+            return snap;
+        }
+        const { connectionInstances, ...rest } = snap;
+        return {
+            ...rest,
+            ...(connectionInstances?.length ? { connectionInstances } : {}),
+        };
+    });
 }
 export function isSessionWithConnections(session) {
     return isBaseSession(session) && 'connectionInstances' in session;

package/esm/Session/DialogQueue.d.ts

@@ -1,7 +1,7 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { DialogComponentType } from '@jbrowse/core/util';
-import type { IAnyStateTreeNode, Instance } from 'mobx-state-tree';
-export declare function DialogQueueSessionMixin(_pluginManager: PluginManager): import("mobx-state-tree").IModelType<{}, {
+import type { IAnyStateTreeNode, Instance } from '@jbrowse/mobx-state-tree';
+export declare function DialogQueueSessionMixin(_pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<{}, {
     queueOfDialogs: [DialogComponentType, unknown][];
 } & {
     readonly DialogComponent: DialogComponentType | undefined;
@@ -9,7 +9,7 @@ export declare function DialogQueueSessionMixin(_pluginManager: PluginManager):
 } & {
     removeActiveDialog(): void;
     queueDialog(cb: (doneCallback: () => void) => [DialogComponentType, unknown]): void;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;
 export type SessionWithDialogsType = ReturnType<typeof DialogQueueSessionMixin>;
 export type SessionWithDialogs = Instance<SessionWithDialogsType>;
 export declare function isSessionWithDialogs(session: IAnyStateTreeNode): session is SessionWithDialogs;

package/esm/Session/DialogQueue.js

@@ -1,5 +1,5 @@
-import { types } from 'mobx-state-tree';
-import { isBaseSession } from './BaseSession';
+import { types } from '@jbrowse/mobx-state-tree';
+import { isBaseSession } from "./BaseSession.js";
 export function DialogQueueSessionMixin(_pluginManager) {
     return types
         .model('DialogQueueSessionMixin', {})
@@ -8,12 +8,10 @@ export function DialogQueueSessionMixin(_pluginManager) {
     }))
         .views(self => ({
         get DialogComponent() {
-            var _a;
-            return (_a = self.queueOfDialogs[0]) === null || _a === void 0 ? void 0 : _a[0];
+            return self.queueOfDialogs[0]?.[0];
         },
         get DialogProps() {
-            var _a;
-            return (_a = self.queueOfDialogs[0]) === null || _a === void 0 ? void 0 : _a[1];
+            return self.queueOfDialogs[0]?.[1];
         },
     }))
         .actions(self => ({

package/esm/Session/DrawerWidgets.d.ts

@@ -1,12 +1,12 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { IAnyStateTreeNode, Instance } from 'mobx-state-tree';
-export declare function DrawerWidgetSessionMixin(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
-    drawerPosition: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    drawerWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
-    widgets: import("mobx-state-tree").IMapType<import("mobx-state-tree").IAnyType>;
-    activeWidgets: import("mobx-state-tree").IMapType<import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>>;
-    minimized: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+import type { IAnyStateTreeNode, Instance } from '@jbrowse/mobx-state-tree';
+export declare function DrawerWidgetSessionMixin(pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<{
+    drawerPosition: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    drawerWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    widgets: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IAnyType>;
+    activeWidgets: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>>;
+    minimized: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
 }, {
     readonly visibleWidget: any;
 } & {
@@ -20,9 +20,17 @@ export declare function DrawerWidgetSessionMixin(pluginManager: PluginManager):
     minimizeWidgetDrawer(): void;
     showWidgetDrawer(): void;
     hideAllWidgets(): void;
-    editConfiguration(configuration: AnyConfigurationModel): void;
+    editConfiguration(configuration: AnyConfigurationModel | {
+        trackId: string;
+    }): void;
     afterAttach(): void;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+    drawerPosition: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    drawerWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    widgets: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IAnyType>;
+    activeWidgets: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>>;
+    minimized: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+}>>;
 export type SessionWithDrawerWidgetsType = ReturnType<typeof DrawerWidgetSessionMixin>;
 export type SessionWithDrawerWidgets = Instance<SessionWithDrawerWidgetsType>;
 export declare function isSessionWithDrawerWidgets(session: IAnyStateTreeNode): session is SessionWithDrawerWidgets;

package/esm/Session/DrawerWidgets.js

@@ -1,8 +1,8 @@
 import { isConfigurationModel } from '@jbrowse/core/configuration';
 import { localStorageGetItem, localStorageSetItem } from '@jbrowse/core/util';
+import { addDisposer, getEnv, isAlive, isStateTreeNode, types, } from '@jbrowse/mobx-state-tree';
 import { autorun } from 'mobx';
-import { addDisposer, isAlive, types } from 'mobx-state-tree';
-import { isBaseSession } from './BaseSession';
+import { isBaseSession } from "./BaseSession.js";
 const minDrawerWidth = 128;
 export function DrawerWidgetSessionMixin(pluginManager) {
     const widgetStateModelType = pluginManager.pluggableMstType('widget', 'stateModel');
@@ -83,18 +83,42 @@ export function DrawerWidgetSessionMixin(pluginManager) {
             self.activeWidgets.clear();
         },
         editConfiguration(configuration) {
-            if (!isConfigurationModel(configuration)) {
-                throw new Error('must pass a configuration model to editConfiguration');
+            let targetConfig;
+            if (isStateTreeNode(configuration) &&
+                isConfigurationModel(configuration)) {
+                targetConfig = configuration;
             }
-            const editor = this.addWidget('ConfigurationEditorWidget', 'configEditor', { target: configuration });
+            else if ('trackId' in configuration) {
+                const trackSchema = pluginManager.pluggableConfigSchemaType('track');
+                targetConfig = trackSchema.create(configuration, getEnv(self));
+            }
+            else {
+                throw new Error('must pass a configuration model or frozen config with trackId to editConfiguration');
+            }
+            const editor = this.addWidget('ConfigurationEditorWidget', 'configEditor', {});
+            editor.setTarget(targetConfig);
             this.showWidget(editor);
         },
         afterAttach() {
-            addDisposer(self, autorun(() => {
+            addDisposer(self, autorun(function drawerPositionAutorun() {
                 localStorageSetItem('drawerPosition', self.drawerPosition);
-            }));
+            }, { name: 'DrawerPosition' }));
         },
-    }));
+    }))
+        .postProcessSnapshot(snap => {
+        if (!snap) {
+            return snap;
+        }
+        const { drawerPosition, drawerWidth, widgets, activeWidgets, minimized, ...rest } = snap;
+        return {
+            ...rest,
+            ...(drawerPosition !== 'right' ? { drawerPosition } : {}),
+            ...(drawerWidth !== 384 ? { drawerWidth } : {}),
+            ...(Object.keys(widgets ?? {}).length ? { widgets } : {}),
+            ...(Object.keys(activeWidgets ?? {}).length ? { activeWidgets } : {}),
+            ...(minimized ? { minimized } : {}),
+        };
+    });
 }
 export function isSessionWithDrawerWidgets(session) {
     return (isBaseSession(session) &&