@jbrowse/product-core 2.17.0 → 3.0.0

package/dist/Session/BaseSession.js

@@ -3,123 +3,61 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.BaseSessionModel = BaseSessionModel;
 exports.isBaseSession = isBaseSession;
 exports.isSession = isSession;
-const mobx_state_tree_1 = require("mobx-state-tree");
 const mst_1 = require("@jbrowse/core/util/types/mst");
-/**
- * #stateModel BaseSessionModel
- *
- * base session shared by all JBrowse products. Be careful what you include
- * here, everything will use it.
- */
+const mobx_state_tree_1 = require("mobx-state-tree");
 function BaseSessionModel(_pluginManager) {
     return mobx_state_tree_1.types
         .model({
-        /**
-         * #property
-         */
         id: mst_1.ElementId,
-        /**
-         * #property
-         */
         name: mobx_state_tree_1.types.string,
-        /**
-         * #property
-         */
         margin: 0,
     })
         .volatile(() => ({
-        /**
-         * #volatile
-         * this is the globally "selected" object. can be anything. code that
-         * wants to deal with this should examine it to see what kind of thing it
-         * is.
-         */
         selection: undefined,
-        /**
-         * #volatile
-         * this is the globally "hovered" object. can be anything. code that
-         * wants to deal with this should examine it to see what kind of thing it
-         * is.
-         */
         hovered: undefined,
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get root() {
             return (0, mobx_state_tree_1.getParent)(self);
         },
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get jbrowse() {
             return self.root.jbrowse;
         },
-        /**
-         * #getter
-         */
         get rpcManager() {
             return self.root.rpcManager;
         },
-        /**
-         * #getter
-         */
         get configuration() {
             return this.jbrowse.configuration;
         },
-        /**
-         * #getter
-         */
         get adminMode() {
             return self.root.adminMode;
         },
-        /**
-         * #getter
-         */
         get textSearchManager() {
             return self.root.textSearchManager;
         },
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get assemblies() {
             return self.jbrowse.assemblies;
         },
     }))
         .actions(self => ({
-        /**
-         * #action
-         * set the global selection, i.e. the globally-selected object. can be a
-         * feature, a view, just about anything
-         */
         setSelection(thing) {
             self.selection = thing;
         },
-        /**
-         * #action
-         * clears the global selection
-         */
         clearSelection() {
             self.selection = undefined;
         },
-        /**
-         * #action
-         */
         setHovered(thing) {
             self.hovered = thing;
         },
     }));
 }
-/** Type guard for BaseSession */
 function isBaseSession(thing) {
     return 'id' in thing && 'name' in thing && 'root' in thing;
 }
-/** Type guard for whether a thing is JBrowse session */
 function isSession(thing) {
     return (0, mobx_state_tree_1.isStateTreeNode)(thing) && isBaseSession(thing);
 }

package/dist/Session/Connections.d.ts

@@ -1,13 +1,8 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import { IAnyStateTreeNode, Instance } from 'mobx-state-tree';
-/**
- * #stateModel ConnectionManagementSessionMixin
- */
+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<{
-    /**
-     * #property
-     */
     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>;
@@ -53,35 +48,8 @@ export declare function ConnectionManagementSessionMixin(pluginManager: PluginMa
         clear(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
 }, {
-    /**
-     * #getter
-     */
-    readonly connections: ({
-        [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">>>)[];
+    readonly connections: BaseConnectionConfigModel[];
 } & {
-    /**
-     * #action
-     */
     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>>;
@@ -179,31 +147,12 @@ export declare function ConnectionManagementSessionMixin(pluginManager: PluginMa
         setTrackConfs(trackConfs: AnyConfigurationModel[]): void;
         clear(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
-    /**
-     * #action
-     */
     prepareToBreakConnection(configuration: AnyConfigurationModel): (Record<string, number> | (() => void))[] | undefined;
-    /**
-     * #action
-     */
     breakConnection(configuration: AnyConfigurationModel): void;
-    /**
-     * #action
-     */
     deleteConnection(configuration: AnyConfigurationModel): any;
-    /**
-     * #action
-     */
     addConnectionConf(connectionConf: AnyConfigurationModel): any;
-    /**
-     * #action
-     */
     clearConnections(): void;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-/** Session mixin MST type for a session that has connections */
 export type SessionWithConnectionsType = ReturnType<typeof ConnectionManagementSessionMixin>;
-/** Instance of a session that has connections: `connectionInstances`,
- * `makeConnection()`, etc. */
 export type SessionWithConnections = Instance<SessionWithConnectionsType>;
-/** Type guard for SessionWithConnections */
 export declare function isSessionWithConnections(session: IAnyStateTreeNode): session is SessionWithConnections;

package/dist/Session/Connections.js

@@ -5,30 +5,18 @@ exports.isSessionWithConnections = isSessionWithConnections;
 const configuration_1 = require("@jbrowse/core/configuration");
 const mobx_state_tree_1 = require("mobx-state-tree");
 const BaseSession_1 = require("./BaseSession");
-/**
- * #stateModel ConnectionManagementSessionMixin
- */
 function ConnectionManagementSessionMixin(pluginManager) {
     return mobx_state_tree_1.types
         .model({
-        /**
-         * #property
-         */
         connectionInstances: mobx_state_tree_1.types.array(pluginManager.pluggableMstType('connection', 'stateModel')),
     })
         .views(self => ({
-        /**
-         * #getter
-         */
         get connections() {
             const { jbrowse } = self;
             return jbrowse.connections;
         },
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         makeConnection(configuration, initialSnapshot = {}) {
             const type = configuration.type;
             if (!type) {
@@ -42,16 +30,11 @@ function ConnectionManagementSessionMixin(pluginManager) {
             const length = self.connectionInstances.push({
                 ...initialSnapshot,
                 name,
-                // @ts-expect-error unsure why ts doesn't like `type` here, but is
-                // needed
                 type,
                 configuration,
             });
             return self.connectionInstances[length - 1];
         },
-        /**
-         * #action
-         */
         prepareToBreakConnection(configuration) {
             const root = self;
             const callbacksToDeref = [];
@@ -75,9 +58,6 @@ function ConnectionManagementSessionMixin(pluginManager) {
                 derefTypeCount,
             ];
         },
-        /**
-         * #action
-         */
         breakConnection(configuration) {
             const name = (0, configuration_1.readConfObject)(configuration, 'name');
             const connection = self.connectionInstances.find(c => c.name === name);
@@ -86,29 +66,19 @@ function ConnectionManagementSessionMixin(pluginManager) {
             }
             self.connectionInstances.remove(connection);
         },
-        /**
-         * #action
-         */
         deleteConnection(configuration) {
             const { jbrowse } = self;
             return jbrowse.deleteConnectionConf(configuration);
         },
-        /**
-         * #action
-         */
         addConnectionConf(connectionConf) {
             const { jbrowse } = self;
             return jbrowse.addConnectionConf(connectionConf);
         },
-        /**
-         * #action
-         */
         clearConnections() {
             self.connectionInstances.clear();
         },
     }));
 }
-/** Type guard for SessionWithConnections */
 function isSessionWithConnections(session) {
     return (0, BaseSession_1.isBaseSession)(session) && 'connectionInstances' in session;
 }

package/dist/Session/DialogQueue.d.ts

@@ -1,34 +1,15 @@
-/** MST mixin for managing a queue of dialogs at the level of the session */
-import PluginManager from '@jbrowse/core/PluginManager';
-import { DialogComponentType } from '@jbrowse/core/util';
-import { IAnyStateTreeNode, Instance } from 'mobx-state-tree';
-/**
- * #stateModel DialogQueueSessionMixin
- */
+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<{}, {
     queueOfDialogs: [DialogComponentType, unknown][];
 } & {
-    /**
-     * #getter
-     */
     readonly DialogComponent: DialogComponentType | undefined;
-    /**
-     * #getter
-     */
     readonly DialogProps: unknown;
 } & {
-    /**
-     * #action
-     */
     removeActiveDialog(): void;
-    /**
-     * #action
-     */
     queueDialog(cb: (doneCallback: () => void) => [DialogComponentType, unknown]): void;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-/** Session mixin MST type for a session that has `queueOfDialogs`, etc. */
 export type SessionWithDialogsType = ReturnType<typeof DialogQueueSessionMixin>;
-/** Instance of a session that has dialogs */
 export type SessionWithDialogs = Instance<SessionWithDialogsType>;
-/** Type guard for SessionWithDialogs */
 export declare function isSessionWithDialogs(session: IAnyStateTreeNode): session is SessionWithDialogs;

package/dist/Session/DialogQueue.js

@@ -1,13 +1,9 @@
 "use strict";
-/** MST mixin for managing a queue of dialogs at the level of the session */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.DialogQueueSessionMixin = DialogQueueSessionMixin;
 exports.isSessionWithDialogs = isSessionWithDialogs;
 const mobx_state_tree_1 = require("mobx-state-tree");
 const BaseSession_1 = require("./BaseSession");
-/**
- * #stateModel DialogQueueSessionMixin
- */
 function DialogQueueSessionMixin(_pluginManager) {
     return mobx_state_tree_1.types
         .model('DialogQueueSessionMixin', {})
@@ -15,31 +11,19 @@ function DialogQueueSessionMixin(_pluginManager) {
         queueOfDialogs: [],
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get DialogComponent() {
             var _a;
             return (_a = self.queueOfDialogs[0]) === null || _a === void 0 ? void 0 : _a[0];
         },
-        /**
-         * #getter
-         */
         get DialogProps() {
             var _a;
             return (_a = self.queueOfDialogs[0]) === null || _a === void 0 ? void 0 : _a[1];
         },
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         removeActiveDialog() {
             self.queueOfDialogs = self.queueOfDialogs.slice(1);
         },
-        /**
-         * #action
-         */
         queueDialog(cb) {
             const [component, props] = cb(() => {
                 this.removeActiveDialog();
@@ -48,7 +32,6 @@ function DialogQueueSessionMixin(_pluginManager) {
         },
     }));
 }
-/** Type guard for SessionWithDialogs */
 function isSessionWithDialogs(session) {
     return (0, BaseSession_1.isBaseSession)(session) && 'queueOfDialogs' in session;
 }

package/dist/Session/DrawerWidgets.d.ts

@@ -1,88 +1,28 @@
-import { IAnyStateTreeNode, Instance } from 'mobx-state-tree';
-import PluginManager from '@jbrowse/core/PluginManager';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-/**
- * #stateModel DrawerWidgetSessionMixin
- */
+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<{
-    /**
-     * #property
-     */
     drawerPosition: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    /**
-     * #property
-     */
     drawerWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
-    /**
-     * #property
-     */
     widgets: import("mobx-state-tree").IMapType<import("mobx-state-tree").IAnyType>;
-    /**
-     * #property
-     */
     activeWidgets: import("mobx-state-tree").IMapType<import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>>;
-    /**
-     * #property
-     */
     minimized: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
 }, {
-    /**
-     * #getter
-     */
     readonly visibleWidget: any;
 } & {
-    /**
-     * #action
-     */
     setDrawerPosition(arg: string): void;
-    /**
-     * #action
-     */
     updateDrawerWidth(drawerWidth: number): number;
-    /**
-     * #action
-     */
     resizeDrawer(distance: number): number;
-    /**
-     * #action
-     */
     addWidget(typeName: string, id: string, initialState?: {}, conf?: unknown): any;
-    /**
-     * #action
-     */
     showWidget(widget: any): void;
-    /**
-     * #action
-     */
     hasWidget(widget: any): boolean;
-    /**
-     * #action
-     */
     hideWidget(widget: any): void;
-    /**
-     * #action
-     */
     minimizeWidgetDrawer(): void;
-    /**
-     * #action
-     */
     showWidgetDrawer(): void;
-    /**
-     * #action
-     */
     hideAllWidgets(): void;
-    /**
-     * #action
-     * opens a configuration editor to configure the given thing,
-     * and sets the current task to be configuring it
-     * @param configuration -
-     */
     editConfiguration(configuration: AnyConfigurationModel): void;
     afterAttach(): void;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-/** Session mixin MST type for a session that manages drawer widgets */
 export type SessionWithDrawerWidgetsType = ReturnType<typeof DrawerWidgetSessionMixin>;
-/** Instance of a session that manages drawer widgets */
 export type SessionWithDrawerWidgets = Instance<SessionWithDrawerWidgetsType>;
-/** Type guard for SessionWithDrawerWidgets */
 export declare function isSessionWithDrawerWidgets(session: IAnyStateTreeNode): session is SessionWithDrawerWidgets;

package/dist/Session/DrawerWidgets.js

@@ -2,63 +2,35 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.DrawerWidgetSessionMixin = DrawerWidgetSessionMixin;
 exports.isSessionWithDrawerWidgets = isSessionWithDrawerWidgets;
-const mobx_state_tree_1 = require("mobx-state-tree");
+const configuration_1 = require("@jbrowse/core/configuration");
 const util_1 = require("@jbrowse/core/util");
 const mobx_1 = require("mobx");
-const configuration_1 = require("@jbrowse/core/configuration");
+const mobx_state_tree_1 = require("mobx-state-tree");
 const BaseSession_1 = require("./BaseSession");
 const minDrawerWidth = 128;
-/**
- * #stateModel DrawerWidgetSessionMixin
- */
 function DrawerWidgetSessionMixin(pluginManager) {
     const widgetStateModelType = pluginManager.pluggableMstType('widget', 'stateModel');
     return mobx_state_tree_1.types
         .model({
-        /**
-         * #property
-         */
         drawerPosition: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.string, () => (0, util_1.localStorageGetItem)('drawerPosition') || 'right'),
-        /**
-         * #property
-         */
         drawerWidth: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.refinement(mobx_state_tree_1.types.integer, width => width >= minDrawerWidth), 384),
-        /**
-         * #property
-         */
         widgets: mobx_state_tree_1.types.map(widgetStateModelType),
-        /**
-         * #property
-         */
         activeWidgets: mobx_state_tree_1.types.map(mobx_state_tree_1.types.safeReference(widgetStateModelType)),
-        /**
-         * #property
-         */
         minimized: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.boolean, false),
     })
         .views(self => ({
-        /**
-         * #getter
-         */
         get visibleWidget() {
             if ((0, mobx_state_tree_1.isAlive)(self)) {
-                // returns most recently added item in active widgets
                 return [...self.activeWidgets.values()][self.activeWidgets.size - 1];
             }
             return undefined;
         },
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         setDrawerPosition(arg) {
             self.drawerPosition = arg;
             localStorage.setItem('drawerPosition', arg);
         },
-        /**
-         * #action
-         */
         updateDrawerWidth(drawerWidth) {
             if (drawerWidth === self.drawerWidth) {
                 return self.drawerWidth;
@@ -70,9 +42,6 @@ function DrawerWidgetSessionMixin(pluginManager) {
             self.drawerWidth = newDrawerWidth;
             return newDrawerWidth;
         },
-        /**
-         * #action
-         */
         resizeDrawer(distance) {
             if (self.drawerPosition === 'left') {
                 distance *= -1;
@@ -81,9 +50,6 @@ function DrawerWidgetSessionMixin(pluginManager) {
             const newDrawerWidth = this.updateDrawerWidth(oldDrawerWidth - distance);
             return oldDrawerWidth - newDrawerWidth;
         },
-        /**
-         * #action
-         */
         addWidget(typeName, id, initialState = {}, conf) {
             const typeDefinition = pluginManager.getElementType('widget', typeName);
             if (!typeDefinition) {
@@ -98,9 +64,6 @@ function DrawerWidgetSessionMixin(pluginManager) {
             self.widgets.set(id, data);
             return self.widgets.get(id);
         },
-        /**
-         * #action
-         */
         showWidget(widget) {
             if (self.activeWidgets.has(widget.id)) {
                 self.activeWidgets.delete(widget.id);
@@ -108,42 +71,21 @@ function DrawerWidgetSessionMixin(pluginManager) {
             self.activeWidgets.set(widget.id, widget);
             self.minimized = false;
         },
-        /**
-         * #action
-         */
         hasWidget(widget) {
             return self.activeWidgets.has(widget.id);
         },
-        /**
-         * #action
-         */
         hideWidget(widget) {
             self.activeWidgets.delete(widget.id);
         },
-        /**
-         * #action
-         */
         minimizeWidgetDrawer() {
             self.minimized = true;
         },
-        /**
-         * #action
-         */
         showWidgetDrawer() {
             self.minimized = false;
         },
-        /**
-         * #action
-         */
         hideAllWidgets() {
             self.activeWidgets.clear();
         },
-        /**
-         * #action
-         * opens a configuration editor to configure the given thing,
-         * and sets the current task to be configuring it
-         * @param configuration -
-         */
         editConfiguration(configuration) {
             if (!(0, configuration_1.isConfigurationModel)(configuration)) {
                 throw new Error('must pass a configuration model to editConfiguration');
@@ -158,7 +100,6 @@ function DrawerWidgetSessionMixin(pluginManager) {
         },
     }));
 }
-/** Type guard for SessionWithDrawerWidgets */
 function isSessionWithDrawerWidgets(session) {
     return ((0, BaseSession_1.isBaseSession)(session) &&
         'widgets' in session &&