@jbrowse/core 2.17.0 → 3.0.0

package/pluggableElementTypes/models/InternetAccountModel.js

@@ -2,153 +2,68 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.InternetAccount = void 0;
 const mobx_state_tree_1 = require("mobx-state-tree");
+const baseInternetAccountConfig_1 = require("./baseInternetAccountConfig");
 const configuration_1 = require("../../configuration");
 const io_1 = require("../../util/io");
 const mst_1 = require("../../util/types/mst");
-const baseInternetAccountConfig_1 = require("./baseInternetAccountConfig");
 const inWebWorker = typeof sessionStorage === 'undefined';
-/**
- * #stateModel BaseInternetAccountModel
- * #category internetAccount
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 exports.InternetAccount = mobx_state_tree_1.types
     .model('InternetAccount', {
-    /**
-     * #property
-     */
     id: mst_1.ElementId,
-    /**
-     * #property
-     */
     type: mobx_state_tree_1.types.string,
-    /**
-     * #property
-     */
     configuration: (0, configuration_1.ConfigurationReference)(baseInternetAccountConfig_1.BaseInternetAccountConfig),
 })
     .views(self => ({
-    /**
-     * #getter
-     */
     get name() {
         return (0, configuration_1.getConf)(self, 'name');
     },
-    /**
-     * #getter
-     */
     get description() {
         return (0, configuration_1.getConf)(self, 'description');
     },
-    /**
-     * #getter
-     */
     get internetAccountId() {
-        return (0, configuration_1.getConf)(self, 'internetAccountId'); // NOTE: this is the explicitIdentifier of the config schema
+        return (0, configuration_1.getConf)(self, 'internetAccountId');
     },
-    /**
-     * #getter
-     */
     get authHeader() {
         return (0, configuration_1.getConf)(self, 'authHeader');
     },
-    /**
-     * #getter
-     */
     get tokenType() {
         return (0, configuration_1.getConf)(self, 'tokenType');
     },
-    /**
-     * #getter
-     */
     get domains() {
         return (0, configuration_1.getConf)(self, 'domains');
     },
-    /**
-     * #getter
-     * Can use this to customize what is displayed in fileSelector's toggle box
-     */
     get toggleContents() {
         return null;
     },
-    /**
-     * #getter
-     * Can use this to customize what the fileSelector. It takes a prop called
-     * `setLocation` that should be used to set a UriLocation
-     */
     get SelectorComponent() {
         return undefined;
     },
-    /**
-     * #getter
-     * Can use this to add a label to the UrlChooser. Has no effect if a custom
-     * SelectorComponent is supplied
-     */
     get selectorLabel() {
         return undefined;
     },
 }))
     .views(self => ({
-    /**
-     * #method
-     * Determine whether this internetAccount provides credentials for a URL
-     * @param location  - UriLocation of resource
-     * @returns true or false
-     */
     handlesLocation(location) {
         return self.domains.some(domain => location.uri.includes(domain));
     },
-    /**
-     * #getter
-     * The key used to store this internetAccount's token in sessionStorage
-     */
     get tokenKey() {
         return `${self.internetAccountId}-token`;
     },
 }))
     .actions(self => ({
-    /**
-     * #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, _reject) {
         throw new Error('getTokenFromUser must be implemented by extending model');
     },
-    /**
-     * #action
-     */
     storeToken(token) {
         sessionStorage.setItem(self.tokenKey, token);
     },
-    /**
-     * #action
-     */
     removeToken() {
         sessionStorage.removeItem(self.tokenKey);
     },
-    /**
-     * #action
-     */
     retrieveToken() {
         return sessionStorage.getItem(self.tokenKey);
     },
-    /**
-     * #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
-     */
     async validateToken(token, _loc) {
         return token;
     },
@@ -156,15 +71,6 @@ exports.InternetAccount = mobx_state_tree_1.types
     .actions(self => {
     let tokenPromise = undefined;
     return {
-        /**
-         * #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
-         */
         async getToken(location) {
             var _a, _b;
             if (tokenPromise) {
@@ -197,9 +103,6 @@ exports.InternetAccount = mobx_state_tree_1.types
     };
 })
     .actions(self => ({
-    /**
-     * #action
-     */
     addAuthHeaderToInit(init, token) {
         return {
             ...init,
@@ -215,14 +118,6 @@ exports.InternetAccount = mobx_state_tree_1.types
             }),
         };
     },
-    /**
-     * #action
-     * Gets the token and returns it along with the information needed to
-     * create a new internetAccount.
-     *
-     * @param location - UriLocation of the resource
-     * @returns
-     */
     async getPreAuthorizationInformation(location) {
         const authToken = await self.getToken(location);
         let validatedToken;
@@ -243,15 +138,6 @@ exports.InternetAccount = mobx_state_tree_1.types
     },
 }))
     .actions(self => ({
-    /**
-     * #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) {
         return async (input, init) => {
             const authToken = await self.getToken(loc);
@@ -261,12 +147,6 @@ exports.InternetAccount = mobx_state_tree_1.types
     },
 }))
     .actions(self => ({
-    /**
-     * #action
-     * Gets a filehandle that uses a fetch that adds auth headers
-     * @param location - UriLocation of the resource
-     * @returns A filehandle
-     */
     openLocation(location) {
         return new io_1.RemoteFileWithRangeCache(location.uri, {
             fetch: self.getFetcher(location),

package/pluggableElementTypes/models/baseConnectionConfig.d.ts

@@ -1,16 +1,10 @@
 import type { Instance } from 'mobx-state-tree';
 declare const BaseConnectionConfig: import("../../configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     name: {
         type: string;
         defaultValue: string;
         description: string;
     };
-    /**
-     * #slot
-     */
     assemblyNames: {
         type: string;
         defaultValue: never[];

package/pluggableElementTypes/models/baseConnectionConfig.js

@@ -1,22 +1,13 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("../../configuration");
-/**
- * #config BaseConnection
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const BaseConnectionConfig = (0, configuration_1.ConfigurationSchema)('BaseConnection', {
-    /**
-     * #slot
-     */
     name: {
         type: 'string',
         defaultValue: 'nameOfConnection',
         description: 'a unique name for this connection',
     },
-    /**
-     * #slot
-     */
     assemblyNames: {
         type: 'stringArray',
         defaultValue: [],
@@ -24,9 +15,6 @@ const BaseConnectionConfig = (0, configuration_1.ConfigurationSchema)('BaseConne
     },
 }, {
     explicitlyTyped: true,
-    /**
-     * #identifier
-     */
     explicitIdentifier: 'connectionId',
 });
 exports.default = BaseConnectionConfig;

package/pluggableElementTypes/models/baseInternetAccountConfig.d.ts

@@ -1,39 +1,24 @@
 export declare const BaseInternetAccountConfig: import("../../configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     name: {
         description: string;
         type: string;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */
     description: {
         description: string;
         type: string;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */
     authHeader: {
         description: string;
         type: string;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */
     tokenType: {
         description: string;
         type: string;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */
     domains: {
         description: string;
         type: string;

package/pluggableElementTypes/models/baseInternetAccountConfig.js

@@ -2,56 +2,34 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.BaseInternetAccountConfig = void 0;
 const configuration_1 = require("../../configuration");
-/**
- * #config BaseInternetAccount
- * the "base" internet account type
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 exports.BaseInternetAccountConfig = (0, configuration_1.ConfigurationSchema)('InternetAccount', {
-    /**
-     * #slot
-     */
     name: {
         description: 'descriptive name of the internet account',
         type: 'string',
         defaultValue: '',
     },
-    /**
-     * #slot
-     */
     description: {
         description: 'a description of the internet account',
         type: 'string',
         defaultValue: '',
     },
-    /**
-     * #slot
-     */
     authHeader: {
         description: 'request header for credentials',
         type: 'string',
         defaultValue: 'Authorization',
     },
-    /**
-     * #slot
-     */
     tokenType: {
         description: 'a custom name for a token to include in the header',
         type: 'string',
         defaultValue: '',
     },
-    /**
-     * #slot
-     */
     domains: {
         description: 'array of valid domains the url can contain to use this account',
         type: 'stringArray',
         defaultValue: [],
     },
 }, {
-    /**
-     * #identifier
-     */
     explicitIdentifier: 'internetAccountId',
     explicitlyTyped: true,
 });

package/pluggableElementTypes/models/baseTrackConfig.d.ts

@@ -1,109 +1,64 @@
-import { Instance } from 'mobx-state-tree';
-import PluginManager from '../../PluginManager';
-/**
- * #config BaseTrack
- */
+import type PluginManager from '../../PluginManager';
+import type { Instance } from 'mobx-state-tree';
 export declare function createBaseTrackConfig(pluginManager: PluginManager): import("../../configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     name: {
         description: string;
         type: string;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */
     assemblyNames: {
         description: string;
         type: string;
         defaultValue: string[];
     };
-    /**
-     * #slot
-     */
     description: {
         description: string;
         type: string;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */
     category: {
         description: string;
         type: string;
         defaultValue: never[];
     };
-    /**
-     * #slot
-     */
     metadata: {
         type: string;
         description: string;
         defaultValue: {};
     };
-    /**
-     * #slot
-     */
     adapter: import("mobx-state-tree").IAnyModelType;
     textSearching: import("../../configuration/configurationSchema").ConfigurationSchemaType<{
-        /**
-         * #slot textSearching.indexedAttributes
-         */
         indexingAttributes: {
             type: string;
             description: string;
             defaultValue: string[];
         };
-        /**
-         * #slot textSearching.indexingFeatureTypesToExclude
-         */
         indexingFeatureTypesToExclude: {
             type: string;
             description: string;
             defaultValue: string[];
         };
-        /**
-         * #slot textSearching.textSearchAdapter
-         */
         textSearchAdapter: import("mobx-state-tree").IAnyModelType;
     }, import("../../configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    /**
-     * #slot
-     */
     displays: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
     formatDetails: import("../../configuration/configurationSchema").ConfigurationSchemaType<{
-        /**
-         * #slot formatDetails.feature
-         */
         feature: {
             type: string;
             description: string;
             defaultValue: {};
             contextVariable: string[];
         };
-        /**
-         * #slot formatDetails.subfeatures
-         */
         subfeatures: {
             type: string;
             description: string;
             defaultValue: {};
             contextVariable: string[];
         };
-        /**
-         * #slot formatDetails.depth
-         */
         depth: {
             type: string;
             defaultValue: number;
             description: string;
         };
-        /**
-         * #slot formatDetails.maxDepth
-         */
         maxDepth: {
             type: string;
             defaultValue: number;
@@ -111,18 +66,12 @@ export declare function createBaseTrackConfig(pluginManager: PluginManager): imp
         };
     }, import("../../configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
     formatAbout: import("../../configuration/configurationSchema").ConfigurationSchemaType<{
-        /**
-         * #slot formatAbout.config
-         */
         config: {
             type: string;
             description: string;
             defaultValue: {};
             contextVariable: string[];
         };
-        /**
-         * #slot formatAbout.hideUris
-         */
         hideUris: {
             type: string;
             defaultValue: boolean;

package/pluggableElementTypes/models/baseTrackConfig.js

@@ -3,111 +3,66 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.createBaseTrackConfig = createBaseTrackConfig;
 const mobx_state_tree_1 = require("mobx-state-tree");
 const configuration_1 = require("../../configuration");
-/**
- * #config BaseTrack
- */
 function createBaseTrackConfig(pluginManager) {
     return (0, configuration_1.ConfigurationSchema)('BaseTrack', {
-        /**
-         * #slot
-         */
         name: {
             description: 'descriptive name of the track',
             type: 'string',
             defaultValue: 'Track',
         },
-        /**
-         * #slot
-         */
         assemblyNames: {
             description: 'name of the assembly (or assemblies) track belongs to',
             type: 'stringArray',
             defaultValue: ['assemblyName'],
         },
-        /**
-         * #slot
-         */
         description: {
             description: 'a description of the track',
             type: 'string',
             defaultValue: '',
         },
-        /**
-         * #slot
-         */
         category: {
             description: 'the category and sub-categories of a track',
             type: 'stringArray',
             defaultValue: [],
         },
-        /**
-         * #slot
-         */
         metadata: {
             type: 'frozen',
             description: 'anything to add about this track',
             defaultValue: {},
         },
-        /**
-         * #slot
-         */
         adapter: pluginManager.pluggableConfigSchemaType('adapter'),
         textSearching: (0, configuration_1.ConfigurationSchema)('textSearching', {
-            /**
-             * #slot textSearching.indexedAttributes
-             */
             indexingAttributes: {
                 type: 'stringArray',
                 description: 'list of which feature attributes to index for text searching',
                 defaultValue: ['Name', 'ID'],
             },
-            /**
-             * #slot textSearching.indexingFeatureTypesToExclude
-             */
             indexingFeatureTypesToExclude: {
                 type: 'stringArray',
                 description: 'list of feature types to exclude in text search index',
                 defaultValue: ['CDS', 'exon'],
             },
-            /**
-             * #slot textSearching.textSearchAdapter
-             */
             textSearchAdapter: pluginManager.pluggableConfigSchemaType('text search adapter'),
         }),
-        /**
-         * #slot
-         */
         displays: mobx_state_tree_1.types.array(pluginManager.pluggableConfigSchemaType('display')),
         formatDetails: (0, configuration_1.ConfigurationSchema)('FormatDetails', {
-            /**
-             * #slot formatDetails.feature
-             */
             feature: {
                 type: 'frozen',
                 description: 'adds extra fields to the feature details',
                 defaultValue: {},
                 contextVariable: ['feature'],
             },
-            /**
-             * #slot formatDetails.subfeatures
-             */
             subfeatures: {
                 type: 'frozen',
                 description: 'adds extra fields to the subfeatures of a feature',
                 defaultValue: {},
                 contextVariable: ['feature'],
             },
-            /**
-             * #slot formatDetails.depth
-             */
             depth: {
                 type: 'number',
                 defaultValue: 2,
                 description: 'depth of subfeatures to iterate the formatter on formatDetails.subfeatures (e.g. you may not want to format the exon/cds subfeatures, so limited to 2',
             },
-            /**
-             * #slot formatDetails.maxDepth
-             */
             maxDepth: {
                 type: 'number',
                 defaultValue: 99999,
@@ -115,18 +70,12 @@ function createBaseTrackConfig(pluginManager) {
             },
         }),
         formatAbout: (0, configuration_1.ConfigurationSchema)('FormatAbout', {
-            /**
-             * #slot formatAbout.config
-             */
             config: {
                 type: 'frozen',
                 description: 'formats configuration object in about dialog',
                 defaultValue: {},
                 contextVariable: ['config'],
             },
-            /**
-             * #slot formatAbout.hideUris
-             */
             hideUris: {
                 type: 'boolean',
                 defaultValue: false,
@@ -134,12 +83,9 @@ function createBaseTrackConfig(pluginManager) {
         }),
     }, {
         preProcessSnapshot: s2 => {
-            const snap = pluginManager.evaluateExtensionPoint('Core-preProcessTrackConfig', JSON.parse(JSON.stringify(s2)));
+            const snap = pluginManager.evaluateExtensionPoint('Core-preProcessTrackConfig', structuredClone(s2));
             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
                 const configDisplayTypes = new Set(displays.map(d => d.type));
                 pluginManager.getTrackType(snap.type).displayTypes.forEach(d => {
                     if (!configDisplayTypes.has(d.name)) {
@@ -152,9 +98,6 @@ function createBaseTrackConfig(pluginManager) {
             }
             return { ...snap, displays };
         },
-        /**
-         * #identifier
-         */
         explicitIdentifier: 'trackId',
         explicitlyTyped: true,
         actions: (self) => ({