@jbrowse/core 2.17.0 → 3.0.0

package/pluggableElementTypes/models/BaseDisplayModel.js

@@ -2,29 +2,15 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.BaseDisplay = void 0;
 const mobx_state_tree_1 = require("mobx-state-tree");
-// locals
 const configuration_1 = require("../../configuration");
-const tracks_1 = require("../../util/tracks");
 const util_1 = require("../../util");
+const tracks_1 = require("../../util/tracks");
 const mst_1 = require("../../util/types/mst");
-/**
- * #stateModel BaseDisplay
- * #category display
- */
 function stateModelFactory() {
     return mobx_state_tree_1.types
         .model('BaseDisplay', {
-        /**
-         * #property
-         */
         id: mst_1.ElementId,
-        /**
-         * #property
-         */
         type: mobx_state_tree_1.types.string,
-        /**
-         * #property
-         */
         rpcDriverName: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
     })
         .volatile(() => ({
@@ -33,29 +19,17 @@ function stateModelFactory() {
         message: undefined,
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get RenderingComponent() {
             const { pluginManager } = (0, util_1.getEnv)(self);
             return pluginManager.getDisplayType(self.type)
                 .ReactComponent;
         },
-        /**
-         * #getter
-         */
         get DisplayBlurb() {
             return null;
         },
-        /**
-         * #getter
-         */
         get adapterConfig() {
             return (0, configuration_1.getConf)(this.parentTrack, 'adapter');
         },
-        /**
-         * #getter
-         */
         get parentTrack() {
             let track = (0, mobx_state_tree_1.getParent)(self);
             while (!(track.configuration && (0, configuration_1.getConf)(track, 'trackId'))) {
@@ -66,11 +40,6 @@ function stateModelFactory() {
             }
             return track;
         },
-        /**
-         * #method
-         * the react props that are passed to the Renderer when data
-         * is rendered in this display
-         */
         renderProps() {
             return {
                 ...(0, tracks_1.getParentRenderProps)(self),
@@ -79,69 +48,33 @@ function stateModelFactory() {
                 displayModel: self,
             };
         },
-        /**
-         * #getter
-         * the pluggable element type object for this display's renderer
-         */
         get rendererType() {
             const { pluginManager } = (0, util_1.getEnv)(self);
             return pluginManager.getRendererType(self.rendererTypeName);
         },
-        /**
-         * #getter
-         * if a display-level message should be displayed instead, make this
-         * return a react component
-         */
         get DisplayMessageComponent() {
             return undefined;
         },
-        /**
-         * #method
-         */
         trackMenuItems() {
             return [];
         },
-        /**
-         * #getter
-         */
         get viewMenuActions() {
             return [];
         },
-        /**
-         * #method
-         * @param region -
-         * @returns falsy if the region is fine to try rendering. Otherwise,
-         * return a react node + string of text. string of text describes why it
-         * cannot be rendered react node allows user to force load at current
-         * setting
-         */
-        regionCannotBeRendered( /* region */) {
+        regionCannotBeRendered() {
             return null;
         },
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         setMessage(arg) {
             self.message = arg;
         },
-        /**
-         * #action
-         */
         setError(error) {
             self.error = error;
         },
-        /**
-         * #action
-         */
         setRpcDriverName(rpcDriverName) {
             self.rpcDriverName = rpcDriverName;
         },
-        /**
-         * #action
-         * base display reload does nothing, see specialized displays for details
-         */
         reload() { },
     }));
 }

package/pluggableElementTypes/models/BaseTrackModel.d.ts

@@ -1,7 +1,7 @@
-import { Instance, IAnyStateTreeNode } from 'mobx-state-tree';
-import { AnyConfigurationSchemaType } from '../../configuration';
-import PluginManager from '../../PluginManager';
-import { MenuItem } from '../../ui';
+import type PluginManager from '../../PluginManager';
+import type { AnyConfigurationSchemaType } from '../../configuration';
+import type { MenuItem } from '../../ui';
+import type { IAnyStateTreeNode, Instance } from 'mobx-state-tree';
 export declare function getCompatibleDisplays(self: IAnyStateTreeNode): ({
     [x: string]: any;
 } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -9,14 +9,6 @@ export declare function getCompatibleDisplays(self: IAnyStateTreeNode): ({
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
 } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>)[];
-/**
- * #stateModel BaseTrackModel
- * #category track
- *
- * these MST models only exist for tracks that are *shown*. they should contain
- * only UI state for the track, and have a reference to a track configuration.
- * note that multiple displayed tracks could use the same configuration.
- */
 export declare function createBaseTrackModel(pm: PluginManager, trackType: string, baseTrackConfig: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<string>;
@@ -24,30 +16,11 @@ export declare function createBaseTrackModel(pm: PluginManager, trackType: strin
     minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     displays: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
 }, {
-    /**
-     * #getter
-     * determines which webworker to send the track to, currently based on trackId
-     */
     readonly rpcSessionId: any;
-    /**
-     * #getter
-     */
     readonly name: any;
-    /**
-     * #getter
-     */
     readonly textSearchAdapter: any;
-    /**
-     * #getter
-     */
     readonly adapterType: import("..").AdapterType;
-    /**
-     * #getter
-     */
     readonly viewMenuActions: MenuItem[];
-    /**
-     * #getter
-     */
     readonly canConfigure: boolean | ({
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -56,26 +29,11 @@ export declare function createBaseTrackModel(pm: PluginManager, trackType: strin
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
     } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>) | undefined;
 } & {
-    /**
-     * #action
-     */
     setMinimized(flag: boolean): void;
-    /**
-     * #action
-     */
     showDisplay(displayId: string, initialSnapshot?: {}): void;
-    /**
-     * #action
-     */
     hideDisplay(displayId: string): number;
-    /**
-     * #action
-     */
     replaceDisplay(oldId: string, newId: string, initialSnapshot?: {}): void;
 } & {
-    /**
-     * #method
-     */
     trackMenuItems(): (import("../../ui").MenuDivider | import("../../ui").MenuSubHeader | import("../../ui").NormalMenuItem | import("../../ui").CheckboxMenuItem | import("../../ui").RadioMenuItem | import("../../ui").SubMenuItem | {
         type: string;
         label: string;

package/pluggableElementTypes/models/BaseTrackModel.js

@@ -4,74 +4,41 @@ exports.getCompatibleDisplays = getCompatibleDisplays;
 exports.createBaseTrackModel = createBaseTrackModel;
 const mobx_1 = require("mobx");
 const mobx_state_tree_1 = require("mobx-state-tree");
-// locals
 const configuration_1 = require("../../configuration");
-const util_1 = require("../../util");
+const util_1 = require("../../data_adapters/util");
+const util_2 = require("../../util");
 const types_1 = require("../../util/types");
 const mst_1 = require("../../util/types/mst");
 function getCompatibleDisplays(self) {
-    const { pluginManager } = (0, util_1.getEnv)(self);
-    const view = (0, util_1.getContainingView)(self);
+    const { pluginManager } = (0, util_2.getEnv)(self);
+    const view = (0, util_2.getContainingView)(self);
     const viewType = pluginManager.getViewType(view.type);
     const compatTypes = new Set(viewType.displayTypes.map(d => d.name));
     const displays = self.configuration.displays;
     return displays.filter(d => compatTypes.has(d.type));
 }
-/**
- * #stateModel BaseTrackModel
- * #category track
- *
- * these MST models only exist for tracks that are *shown*. they should contain
- * only UI state for the track, and have a reference to a track configuration.
- * note that multiple displayed tracks could use the same configuration.
- */
 function createBaseTrackModel(pm, trackType, baseTrackConfig) {
     return mobx_state_tree_1.types
         .model(trackType, {
-        /**
-         * #property
-         */
         id: mst_1.ElementId,
-        /**
-         * #property
-         */
         type: mobx_state_tree_1.types.literal(trackType),
-        /**
-         * #property
-         */
         configuration: (0, configuration_1.ConfigurationReference)(baseTrackConfig),
-        /**
-         * #property
-         */
         minimized: false,
-        /**
-         * #property
-         */
         displays: mobx_state_tree_1.types.array(pm.pluggableMstType('display', 'stateModel')),
     })
         .views(self => ({
-        /**
-         * #getter
-         * determines which webworker to send the track to, currently based on trackId
-         */
         get rpcSessionId() {
-            return self.configuration.trackId;
+            const adapter = (0, configuration_1.getConf)(self, 'adapter');
+            return adapter
+                ? (0, util_1.adapterConfigCacheKey)(adapter)
+                : self.configuration.trackId;
         },
-        /**
-         * #getter
-         */
         get name() {
             return (0, configuration_1.getConf)(self, 'name');
         },
-        /**
-         * #getter
-         */
         get textSearchAdapter() {
             return (0, configuration_1.getConf)(self, 'textSearchAdapter');
         },
-        /**
-         * #getter
-         */
         get adapterType() {
             const adapterConfig = (0, configuration_1.getConf)(self, 'adapter');
             if (!adapterConfig) {
@@ -83,17 +50,11 @@ function createBaseTrackModel(pm, trackType, baseTrackConfig) {
             }
             return adapterType;
         },
-        /**
-         * #getter
-         */
         get viewMenuActions() {
             return self.displays.flatMap(d => d.viewMenuActions);
         },
-        /**
-         * #getter
-         */
         get canConfigure() {
-            const session = (0, util_1.getSession)(self);
+            const session = (0, util_2.getSession)(self);
             const { sessionTracks, adminMode } = session;
             return ((0, types_1.isSessionModelWithConfigEditing)(session) &&
                 (adminMode ||
@@ -101,15 +62,9 @@ function createBaseTrackModel(pm, trackType, baseTrackConfig) {
         },
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         setMinimized(flag) {
             self.minimized = flag;
         },
-        /**
-         * #action
-         */
         showDisplay(displayId, initialSnapshot = {}) {
             const schema = pm.pluggableConfigSchemaType('display');
             const conf = (0, mobx_state_tree_1.resolveIdentifier)(schema, (0, mobx_state_tree_1.getRoot)(self), displayId);
@@ -124,9 +79,6 @@ function createBaseTrackModel(pm, trackType, baseTrackConfig) {
             });
             self.displays.push(display);
         },
-        /**
-         * #action
-         */
         hideDisplay(displayId) {
             const schema = pm.pluggableConfigSchemaType('display');
             const conf = (0, mobx_state_tree_1.resolveIdentifier)(schema, (0, mobx_state_tree_1.getRoot)(self), displayId);
@@ -136,9 +88,6 @@ function createBaseTrackModel(pm, trackType, baseTrackConfig) {
             });
             return t.length;
         },
-        /**
-         * #action
-         */
         replaceDisplay(oldId, newId, initialSnapshot = {}) {
             const idx = self.displays.findIndex(d => d.configuration.displayId === oldId);
             if (idx === -1) {
@@ -158,9 +107,6 @@ function createBaseTrackModel(pm, trackType, baseTrackConfig) {
         },
     }))
         .views(self => ({
-        /**
-         * #method
-         */
         trackMenuItems() {
             const menuItems = self.displays.flatMap(d => d.trackMenuItems());
             const shownId = self.displays[0].configuration.displayId;

package/pluggableElementTypes/models/BaseViewModel.d.ts

@@ -1,5 +1,5 @@
-import { Instance } from 'mobx-state-tree';
-import { MenuItem } from '../../ui';
+import type { MenuItem } from '../../ui';
+import type { Instance } from 'mobx-state-tree';
 declare const BaseViewModel: import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -7,30 +7,10 @@ declare const BaseViewModel: import("mobx-state-tree").IModelType<{
 }, {
     width: number;
 } & {
-    /**
-     * #getter
-     */
     menuItems(): MenuItem[];
 } & {
-    /**
-     * #action
-     */
     setDisplayName(name: string): void;
-    /**
-     * #action
-     * width is an important attribute of the view model, when it becomes set, it
-     * often indicates when the app can start drawing to it. certain views like
-     * lgv are strict about this because if it tries to draw before it knows the
-     * width it should draw to, it may start fetching data for regions it doesn't
-     * need to
-     *
-     * setWidth is updated by a ResizeObserver generally, the views often need
-     * to know how wide they are to properly draw genomic regions
-     */
     setWidth(newWidth: number): void;
-    /**
-     * #action
-     */
     setMinimized(flag: boolean): void;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export default BaseViewModel;
@@ -53,30 +33,10 @@ export declare const BaseViewModelWithDisplayedRegions: import("mobx-state-tree"
 }, {
     width: number;
 } & {
-    /**
-     * #getter
-     */
     menuItems(): MenuItem[];
 } & {
-    /**
-     * #action
-     */
     setDisplayName(name: string): void;
-    /**
-     * #action
-     * width is an important attribute of the view model, when it becomes set, it
-     * often indicates when the app can start drawing to it. certain views like
-     * lgv are strict about this because if it tries to draw before it knows the
-     * width it should draw to, it may start fetching data for regions it doesn't
-     * need to
-     *
-     * setWidth is updated by a ResizeObserver generally, the views often need
-     * to know how wide they are to properly draw genomic regions
-     */
     setWidth(newWidth: number): void;
-    /**
-     * #action
-     */
     setMinimized(flag: boolean): void;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export type IBaseViewModelWithDisplayedRegions = Instance<typeof BaseViewModelWithDisplayedRegions>;

package/pluggableElementTypes/models/BaseViewModel.js

@@ -3,69 +3,33 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.BaseViewModelWithDisplayedRegions = void 0;
 const mobx_state_tree_1 = require("mobx-state-tree");
 const mst_1 = require("../../util/types/mst");
-const mst_2 = require("../../util/types/mst");
-/**
- * #stateModel BaseViewModel
- * #category view
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const BaseViewModel = mobx_state_tree_1.types
     .model('BaseView', {
-    /**
-     * #property
-     */
     id: mst_1.ElementId,
-    /**
-     * #property
-     * displayName is displayed in the header of the view, or assembly names
-     * being used if none is specified
-     */
     displayName: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
-    /**
-     * #property
-     */
     minimized: false,
 })
     .volatile(() => ({
     width: 800,
 }))
     .views(() => ({
-    /**
-     * #getter
-     */
     menuItems() {
         return [];
     },
 }))
     .actions(self => ({
-    /**
-     * #action
-     */
     setDisplayName(name) {
         self.displayName = name;
     },
-    /**
-     * #action
-     * width is an important attribute of the view model, when it becomes set, it
-     * often indicates when the app can start drawing to it. certain views like
-     * lgv are strict about this because if it tries to draw before it knows the
-     * width it should draw to, it may start fetching data for regions it doesn't
-     * need to
-     *
-     * setWidth is updated by a ResizeObserver generally, the views often need
-     * to know how wide they are to properly draw genomic regions
-     */
     setWidth(newWidth) {
         self.width = newWidth;
     },
-    /**
-     * #action
-     */
     setMinimized(flag) {
         self.minimized = flag;
     },
 }));
 exports.default = BaseViewModel;
 exports.BaseViewModelWithDisplayedRegions = BaseViewModel.props({
-    displayedRegions: mobx_state_tree_1.types.array(mst_2.Region),
+    displayedRegions: mobx_state_tree_1.types.array(mst_1.Region),
 });

package/pluggableElementTypes/models/InternetAccountModel.d.ts

@@ -1,19 +1,10 @@
-import React from 'react';
-import { Instance } from 'mobx-state-tree';
+import type React from 'react';
 import { RemoteFileWithRangeCache } from '../../util/io';
-import { UriLocation, AnyReactComponentType } from '../../util/types';
+import type { AnyReactComponentType, UriLocation } from '../../util/types';
+import type { Instance } from 'mobx-state-tree';
 export declare const InternetAccount: import("mobx-state-tree").IModelType<{
-    /**
-     * #property
-     */
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    /**
-     * #property
-     */
     type: import("mobx-state-tree").ISimpleType<string>;
-    /**
-     * #property
-     */
     configuration: import("../../configuration/configurationSchema").ConfigurationSchemaType<{
         name: {
             description: string;
@@ -42,111 +33,27 @@ export declare const InternetAccount: import("mobx-state-tree").IModelType<{
         };
     }, import("../../configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "internetAccountId">>;
 }, {
-    /**
-     * #getter
-     */
     readonly name: string;
-    /**
-     * #getter
-     */
     readonly description: string;
-    /**
-     * #getter
-     */
     readonly internetAccountId: string;
-    /**
-     * #getter
-     */
     readonly authHeader: string;
-    /**
-     * #getter
-     */
     readonly tokenType: string;
-    /**
-     * #getter
-     */
     readonly domains: string[];
-    /**
-     * #getter
-     * Can use this to customize what is displayed in fileSelector's toggle box
-     */
     readonly toggleContents: React.ReactNode;
-    /**
-     * #getter
-     * Can use this to customize what the fileSelector. It takes a prop called
-     * `setLocation` that should be used to set a UriLocation
-     */
     readonly SelectorComponent: AnyReactComponentType | undefined;
-    /**
-     * #getter
-     * Can use this to add a label to the UrlChooser. Has no effect if a custom
-     * SelectorComponent is supplied
-     */
     readonly selectorLabel: string | undefined;
 } & {
-    /**
-     * #method
-     * Determine whether this internetAccount provides credentials for a URL
-     * @param location  - UriLocation of resource
-     * @returns true or false
-     */
     handlesLocation(location: UriLocation): boolean;
-    /**
-     * #getter
-     * The key used to store this internetAccount's token in sessionStorage
-     */
     readonly tokenKey: string;
 } & {
-    /**
-     * #action
-     * Must be implemented by a model extending or composing this one. Pass the
-     * user's token to `resolve`.
-     * @param resolve - Pass the token to this function
-     * @param reject - If there is an error getting the token, call this function
-     */
     getTokenFromUser(_resolve: (token: string) => void, _reject: (error: Error) => void): void;
-    /**
-     * #action
-     */
     storeToken(token: string): void;
-    /**
-     * #action
-     */
     removeToken(): void;
-    /**
-     * #action
-     */
     retrieveToken(): string | null;
-    /**
-     * #action
-     * This can be used by an internetAccount to validate a token works before
-     * it is used. This is run when preAuthorizationInformation is requested,
-     * so it can be used to check that a token is valid before sending it to a
-     * worker thread. It expects the token to be returned so that this action
-     * can also be used to generate a new token (e.g. by using a refresh token)
-     * if the original one was invalid. Should throw an error if a token is
-     * invalid.
-     *
-     * @param token - Auth token
-     * @param loc - UriLocation of the resource
-     * @returns - Valid auth token
-     */
     validateToken(token: string, _loc: UriLocation): Promise<string>;
 } & {
-    /**
-     * #action
-     * Try to get the token from the location pre-auth, from local storage,
-     * or from a previously cached promise. If token is not available, uses
-     * `getTokenFromUser`.
-     *
-     * @param location - UriLocation of the resource
-     * @returns A promise for the token
-     */
     getToken(location?: UriLocation): Promise<string>;
 } & {
-    /**
-     * #action
-     */
     addAuthHeaderToInit(init?: RequestInit, token?: string): {
         headers: Headers;
         body?: BodyInit | null;
@@ -163,14 +70,6 @@ export declare const InternetAccount: import("mobx-state-tree").IModelType<{
         signal?: AbortSignal | null;
         window?: null;
     };
-    /**
-     * #action
-     * Gets the token and returns it along with the information needed to
-     * create a new internetAccount.
-     *
-     * @param location - UriLocation of the resource
-     * @returns
-     */
     getPreAuthorizationInformation(location: UriLocation): Promise<{
         internetAccountType: string;
         authInfo: {
@@ -179,23 +78,8 @@ export declare const InternetAccount: import("mobx-state-tree").IModelType<{
         };
     }>;
 } & {
-    /**
-     * #action
-     * Get a fetch method that will add any needed authentication headers to
-     * the request before sending it. If location is provided, it will be
-     * checked to see if it includes a token in it pre-auth information.
-     *
-     * @param loc - UriLocation of the resource
-     * @returns A function that can be used to fetch
-     */
     getFetcher(loc?: UriLocation): (input: RequestInfo, init?: RequestInit) => Promise<Response>;
 } & {
-    /**
-     * #action
-     * Gets a filehandle that uses a fetch that adds auth headers
-     * @param location - UriLocation of the resource
-     * @returns A filehandle
-     */
     openLocation(location: UriLocation): RemoteFileWithRangeCache;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export type BaseInternetAccountStateModel = typeof InternetAccount;