@jbrowse/core 2.5.0 → 2.6.0

package/pluggableElementTypes/models/BaseConnectionModelFactory.js

@@ -1,6 +1,11 @@
 "use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
 Object.defineProperty(exports, "__esModule", { value: true });
 const mobx_state_tree_1 = require("mobx-state-tree");
+const configuration_1 = require("../../configuration");
+const baseConnectionConfig_1 = __importDefault(require("./baseConnectionConfig"));
 /**
  * #stateModel BaseConnectionModel
  */
@@ -15,6 +20,10 @@ function stateModelFactory(pluginManager) {
          * #property
          */
         tracks: mobx_state_tree_1.types.array(pluginManager.pluggableConfigSchemaType('track')),
+        /**
+         * #property
+         */
+        configuration: (0, configuration_1.ConfigurationReference)(baseConnectionConfig_1.default),
     })
         .actions(self => ({
         afterAttach() {

package/pluggableElementTypes/models/BaseDisplayModel.d.ts

@@ -17,6 +17,7 @@ export declare const BaseDisplay: import("mobx-state-tree").IModelType<{
 }, {
     rendererTypeName: string;
     error: unknown;
+    message: string | undefined;
 } & {
     /**
      * #getter
@@ -29,6 +30,7 @@ export declare const BaseDisplay: import("mobx-state-tree").IModelType<{
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
+            message: string | undefined;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
             /**
              * #property
@@ -45,6 +47,7 @@ export declare const BaseDisplay: import("mobx-state-tree").IModelType<{
         }, {
             rendererTypeName: string;
             error: unknown;
+            message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
         onHorizontalScroll?: Function | undefined;
         blockState?: Record<string, any> | undefined;
@@ -60,6 +63,7 @@ export declare const BaseDisplay: import("mobx-state-tree").IModelType<{
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
+            message: string | undefined;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
             /**
              * #property
@@ -76,6 +80,7 @@ export declare const BaseDisplay: import("mobx-state-tree").IModelType<{
         }, {
             rendererTypeName: string;
             error: unknown;
+            message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }> | null;
     /**
@@ -120,8 +125,12 @@ export declare const BaseDisplay: import("mobx-state-tree").IModelType<{
      *  string of text describes why it cannot be rendered
      *  react node allows user to force load at current setting
      */
-    regionCannotBeRendered(): undefined;
+    regionCannotBeRendered(): null;
 } & {
+    /**
+     * #action
+     */
+    setMessage(arg?: string): void;
     /**
      * #action
      */

package/pluggableElementTypes/models/BaseDisplayModel.js

@@ -9,6 +9,7 @@ const util_1 = require("../../util");
 const mst_1 = require("../../util/types/mst");
 /**
  * #stateModel BaseDisplay
+ * #category display
  */
 function stateModelFactory() {
     return mobx_state_tree_1.types
@@ -29,6 +30,7 @@ function stateModelFactory() {
         .volatile(() => ({
         rendererTypeName: '',
         error: undefined,
+        message: undefined,
     }))
         .views(self => ({
         /**
@@ -122,10 +124,16 @@ function stateModelFactory() {
          *  react node allows user to force load at current setting
          */
         regionCannotBeRendered( /* region */) {
-            return undefined;
+            return null;
         },
     }))
         .actions(self => ({
+        /**
+         * #action
+         */
+        setMessage(arg) {
+            self.message = arg;
+        },
         /**
          * #action
          */

package/pluggableElementTypes/models/BaseTrackModel.d.ts

@@ -9,6 +9,7 @@ export declare function getCompatibleDisplays(self: IAnyStateTreeNode): ({
 } & 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.

package/pluggableElementTypes/models/BaseTrackModel.js

@@ -19,6 +19,7 @@ function getCompatibleDisplays(self) {
 exports.getCompatibleDisplays = getCompatibleDisplays;
 /**
  * #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.

package/pluggableElementTypes/models/BaseViewModel.d.ts

@@ -34,5 +34,49 @@ declare const BaseViewModel: import("mobx-state-tree").IModelType<{
     setMinimized(flag: boolean): void;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export default BaseViewModel;
-export interface IBaseViewModel extends Instance<typeof BaseViewModel> {
-}
+export type IBaseViewModel = Instance<typeof BaseViewModel>;
+export declare const BaseViewModelWithDisplayedRegions: 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>>;
+    minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+} & {
+    displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
+        refName: import("mobx-state-tree").ISimpleType<string>;
+        start: import("mobx-state-tree").ISimpleType<number>;
+        end: import("mobx-state-tree").ISimpleType<number>;
+        reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    } & {
+        assemblyName: import("mobx-state-tree").ISimpleType<string>;
+    }, {
+        setRefName(newRefName: string): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+}, {
+    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

@@ -1,9 +1,12 @@
 "use strict";
 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
 const BaseViewModel = mobx_state_tree_1.types
@@ -63,3 +66,6 @@ const BaseViewModel = mobx_state_tree_1.types
     },
 }));
 exports.default = BaseViewModel;
+exports.BaseViewModelWithDisplayedRegions = BaseViewModel.props({
+    displayedRegions: mobx_state_tree_1.types.array(mst_2.Region),
+});

package/pluggableElementTypes/models/InternetAccountModel.d.ts

@@ -120,12 +120,13 @@ export declare const InternetAccount: import("mobx-state-tree").IModelType<{
     /**
      * #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
+     * 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
@@ -137,6 +138,7 @@ export declare const InternetAccount: import("mobx-state-tree").IModelType<{
      * 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
      */
@@ -164,6 +166,7 @@ export declare const InternetAccount: import("mobx-state-tree").IModelType<{
      * #action
      * Gets the token and returns it along with the information needed to
      * create a new internetAccount.
+     *
      * @param location - UriLocation of the resource
      * @returns
      */
@@ -180,6 +183,7 @@ export declare const InternetAccount: import("mobx-state-tree").IModelType<{
      * 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
      */

package/pluggableElementTypes/models/InternetAccountModel.js

@@ -9,6 +9,7 @@ const baseInternetAccountConfig_1 = require("./baseInternetAccountConfig");
 const inWebWorker = typeof sessionStorage === 'undefined';
 /**
  * #stateModel BaseInternetAccountModel
+ * #category internetAccount
  */
 function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
 exports.InternetAccount = mobx_state_tree_1.types
@@ -137,12 +138,13 @@ exports.InternetAccount = mobx_state_tree_1.types
     /**
      * #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
+     * 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
@@ -159,6 +161,7 @@ exports.InternetAccount = mobx_state_tree_1.types
          * 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
          */
@@ -180,17 +183,13 @@ exports.InternetAccount = mobx_state_tree_1.types
                 tokenPromise = Promise.resolve(token);
                 return tokenPromise;
             }
-            tokenPromise = new Promise((r, x) => {
-                function resolve(token) {
-                    self.storeToken(token);
-                    r(token);
-                }
-                function reject(error) {
-                    self.removeToken();
-                    x(error);
-                }
-                self.getTokenFromUser(resolve, reject);
-            });
+            tokenPromise = new Promise((resolve, reject) => self.getTokenFromUser(token => {
+                self.storeToken(token);
+                resolve(token);
+            }, error => {
+                self.removeToken();
+                reject(error);
+            }));
             return tokenPromise;
         },
     };
@@ -200,17 +199,21 @@ exports.InternetAccount = mobx_state_tree_1.types
      * #action
      */
     addAuthHeaderToInit(init = {}, token) {
-        const tokenInfoString = self.tokenType
-            ? `${self.tokenType} ${token}`
-            : token;
-        const newHeaders = new Headers(init.headers || {});
-        newHeaders.append(self.authHeader, tokenInfoString);
-        return { ...init, headers: newHeaders };
+        return {
+            ...init,
+            headers: new Headers({
+                ...init.headers,
+                [self.authHeader]: self.tokenType
+                    ? `${self.tokenType} ${token}`
+                    : token,
+            }),
+        };
     },
     /**
      * #action
      * Gets the token and returns it along with the information needed to
      * create a new internetAccount.
+     *
      * @param location - UriLocation of the resource
      * @returns
      */
@@ -226,7 +229,10 @@ exports.InternetAccount = mobx_state_tree_1.types
         }
         return {
             internetAccountType: self.type,
-            authInfo: { token: validatedToken, configuration: (0, configuration_1.getConf)(self) },
+            authInfo: {
+                token: validatedToken,
+                configuration: (0, configuration_1.getConf)(self),
+            },
         };
     },
 }))
@@ -236,6 +242,7 @@ exports.InternetAccount = mobx_state_tree_1.types
      * 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
      */

package/pluggableElementTypes/models/baseConnectionConfig.d.ts

@@ -1,4 +1,5 @@
-declare const _default: import("../../configuration/configurationSchema").ConfigurationSchemaType<{
+import type { Instance } from 'mobx-state-tree';
+declare const BaseConnectionConfig: import("../../configuration/configurationSchema").ConfigurationSchemaType<{
     /**
      * #slot
      */
@@ -16,4 +17,6 @@ declare const _default: import("../../configuration/configurationSchema").Config
         description: string;
     };
 }, import("../../configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
-export default _default;
+export default BaseConnectionConfig;
+export type BaseConnectionConfigSchema = typeof BaseConnectionConfig;
+export type BaseConnectionConfigModel = Instance<BaseConnectionConfigSchema>;

package/pluggableElementTypes/models/baseConnectionConfig.js

@@ -5,7 +5,7 @@ const configuration_1 = require("../../configuration");
  * #config BaseConnection
  */
 function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
-exports.default = (0, configuration_1.ConfigurationSchema)('BaseConnection', {
+const BaseConnectionConfig = (0, configuration_1.ConfigurationSchema)('BaseConnection', {
     /**
      * #slot
      */
@@ -29,3 +29,4 @@ exports.default = (0, configuration_1.ConfigurationSchema)('BaseConnection', {
      */
     explicitIdentifier: 'connectionId',
 });
+exports.default = BaseConnectionConfig;

package/pluggableElementTypes/models/baseInternetAccountConfig.js

@@ -3,7 +3,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.BaseInternetAccountConfig = void 0;
 const configuration_1 = require("../../configuration");
 /**
- * #config InternetAccount
+ * #config BaseInternetAccount
  * the "base" internet account type
  */
 function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars

package/pluggableElementTypes/models/baseTrackConfig.d.ts

@@ -121,5 +121,5 @@ export declare function createBaseTrackConfig(pluginManager: PluginManager): imp
         };
     }, import("../../configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 }, import("../../configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>;
-export type BaseTrackConfigModel = ReturnType<typeof createBaseTrackConfig>;
-export type BaseTrackConfig = Instance<BaseTrackConfigModel>;
+export type BaseTrackConfigSchema = ReturnType<typeof createBaseTrackConfig>;
+export type BaseTrackConfig = Instance<BaseTrackConfigSchema>;

package/pluggableElementTypes/models/baseTrackConfig.js

@@ -1,7 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.createBaseTrackConfig = void 0;
-/* eslint-disable @typescript-eslint/no-explicit-any */
 const mobx_state_tree_1 = require("mobx-state-tree");
 const configuration_1 = require("../../configuration");
 /**
@@ -126,15 +125,15 @@ function createBaseTrackConfig(pluginManager) {
             },
         }),
     }, {
-        preProcessSnapshot: s => {
-            const snap = JSON.parse(JSON.stringify(s));
+        preProcessSnapshot: s2 => {
+            const snap = pluginManager.evaluateExtensionPoint('Core-preProcessTrackConfig', JSON.parse(JSON.stringify(s2)));
             const displayTypes = new Set();
             const { displays = [] } = snap;
             if (snap.trackId !== 'placeholderId') {
                 // Gets the displays on the track snapshot and the possible displays
                 // from the track type and adds any missing possible displays to the
                 // snapshot
-                displays.forEach((d) => d && displayTypes.add(d.type));
+                displays.forEach(d => d && displayTypes.add(d.type));
                 const trackType = pluginManager.getTrackType(snap.type);
                 trackType.displayTypes.forEach(displayType => {
                     if (!displayTypes.has(displayType.name)) {
@@ -152,13 +151,16 @@ function createBaseTrackConfig(pluginManager) {
          */
         explicitIdentifier: 'trackId',
         explicitlyTyped: true,
+        // eslint-disable-next-line @typescript-eslint/no-explicit-any
         actions: (self) => ({
             addDisplayConf(conf) {
                 const { type } = conf;
                 if (!type) {
                     throw new Error(`unknown display type ${type}`);
                 }
-                const display = self.displays.find((d) => (d === null || d === void 0 ? void 0 : d.displayId) === conf.displayId);
+                const display = self.displays.find(
+                // eslint-disable-next-line @typescript-eslint/no-explicit-any
+                (d) => (d === null || d === void 0 ? void 0 : d.displayId) === conf.displayId);
                 if (display) {
                     return display;
                 }

package/pluggableElementTypes/models/index.d.ts

@@ -10,4 +10,4 @@ export { BaseInternetAccountConfig } from './baseInternetAccountConfig';
 export { createBaseTrackModel } from './BaseTrackModel';
 export type { BaseTrackModel, BaseTrackStateModel } from './BaseTrackModel';
 export { createBaseTrackConfig } from './baseTrackConfig';
-export type { BaseTrackConfig, BaseTrackConfigModel } from './baseTrackConfig';
+export type { BaseTrackConfig, BaseTrackConfigSchema as BaseTrackConfigModel, } from './baseTrackConfig';

package/pluggableElementTypes/renderers/BoxRendererType.js

@@ -113,8 +113,7 @@ class BoxRendererType extends FeatureRendererType_1.default {
     createLayoutInWorker(args) {
         const { regions } = args;
         const session = this.getWorkerSession(args);
-        const subLayout = session.layout.getSublayout(regions[0].refName);
-        return subLayout;
+        return session.layout.getSublayout(regions[0].refName);
     }
     serializeResultsInWorker(results, args) {
         const serialized = super.serializeResultsInWorker(results, args);

package/pluggableElementTypes/renderers/CircularChordRendererType.d.ts

@@ -1,3 +1,4 @@
+import React from 'react';
 import { SimpleFeature, SimpleFeatureSerialized } from '../../util';
 import FeatureRenderer from './FeatureRendererType';
 export default class CircularChordRendererType extends FeatureRenderer {
@@ -16,7 +17,7 @@ export default class CircularChordRendererType extends FeatureRenderer {
     } | {
         features: Map<string, SimpleFeature>;
         blockKey: string;
-        reactElement: JSX.Element;
+        reactElement: React.JSX.Element;
         html: string;
     };
 }

package/pluggableElementTypes/renderers/FeatureRendererType.d.ts

@@ -87,5 +87,7 @@ export default class FeatureRendererType extends ServerSideRendererType {
      *
      * @param props - render args
      */
-    render(props: RenderArgsDeserialized): Promise<RenderResults>;
+    render(props: RenderArgsDeserialized & {
+        features?: Map<string, Feature>;
+    }): Promise<RenderResults>;
 }

package/pluggableElementTypes/renderers/FeatureRendererType.js

@@ -120,10 +120,9 @@ class FeatureRendererType extends ServerSideRendererType_1.default {
      * @returns true if this feature passes all configured filters
      */
     featurePassesFilters(renderArgs, feature) {
-        if (!renderArgs.filters) {
-            return true;
-        }
-        return renderArgs.filters.passes(feature, renderArgs);
+        return renderArgs.filters
+            ? renderArgs.filters.passes(feature, renderArgs)
+            : true;
     }
     /**
      * gets features and renders
@@ -131,8 +130,7 @@ class FeatureRendererType extends ServerSideRendererType_1.default {
      * @param props - render args
      */
     async render(props) {
-        const features = props.features ||
-            (await this.getFeatures(props));
+        const features = props.features || (await this.getFeatures(props));
         const result = await super.render({ ...props, features });
         return { ...result, features };
     }

package/pluggableElementTypes/renderers/RpcRenderedSvgGroup.d.ts

@@ -1,7 +1,8 @@
+import React from 'react';
 import { AnyReactComponentType, Feature } from '../../util';
 declare const _default: (props: {
     html: string;
     features: Map<string, Feature>;
     RenderingComponent: AnyReactComponentType;
-}) => JSX.Element;
+}) => React.JSX.Element;
 export default _default;

package/pluggableElementTypes/renderers/ServerSideRenderedContent.d.ts

@@ -3,5 +3,5 @@ import { ResultsSerialized, RenderArgs } from './ServerSideRendererType';
 interface Props extends ResultsSerialized, RenderArgs {
     RenderingComponent: React.ComponentType<any>;
 }
-export default function ({ theme, html, RenderingComponent, ...rest }: Props): JSX.Element;
+export default function ({ theme, html, RenderingComponent, ...rest }: Props): React.JSX.Element;
 export {};

package/rpc/BaseRpcDriver.js

@@ -6,13 +6,7 @@ const util_1 = require("../util");
 const remoteAbortSignals_1 = require("./remoteAbortSignals");
 const configuration_1 = require("../configuration");
 function isClonable(thing) {
-    if (typeof thing === 'function') {
-        return false;
-    }
-    if (thing instanceof Error) {
-        return false;
-    }
-    return true;
+    return !(typeof thing === 'function') && !(thing instanceof Error);
 }
 // watches the given worker object, returns a promise that will be rejected if
 // the worker times out