@jbrowse/core 1.6.4 → 1.6.7

package/BaseFeatureWidget/BaseFeatureDetail.js

@@ -29,8 +29,6 @@ var _core = require("@material-ui/core");
 
 var _ExpandMore = _interopRequireDefault(require("@material-ui/icons/ExpandMore"));
 
-var _styles = require("@material-ui/core/styles");
-
 var _xDataGrid = require("@mui/x-data-grid");
 
 var _mobxReact = require("mobx-react");
@@ -64,7 +62,7 @@ var MAX_FIELD_NAME_WIDTH = 170; // these are always omitted as too detailed
 var globalOmit = ['length', 'position', 'subfeatures', 'uniqueId', 'exonFrames', 'parentId', 'thickStart', 'thickEnd']; // coreDetails are omitted in some circumstances
 
 var coreDetails = ['name', 'start', 'end', 'strand', 'refName', 'description', 'type'];
-var useStyles = (0, _styles.makeStyles)(function (theme) {
+var useStyles = (0, _core.makeStyles)(function (theme) {
   return {
     expansionPanelDetails: {
       display: 'block',

package/BaseFeatureWidget/index.d.ts

@@ -1,5 +1,5 @@
 import PluginManager from '../PluginManager';
-declare const configSchema: import("../configuration/configurationSchema").AnyConfigurationSchemaType;
+declare const configSchema: import("../configuration").AnyConfigurationSchemaType;
 export default function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;

package/PluginLoader.d.ts

@@ -1,5 +1,5 @@
 import { PluginConstructor } from './Plugin';
-export declare const PluginSourceConfigurationSchema: import("./configuration/configurationSchema").AnyConfigurationSchemaType;
+export declare const PluginSourceConfigurationSchema: import("./configuration").AnyConfigurationSchemaType;
 export interface UMDPluginDefinition {
     umdUrl: string;
     name: string;

package/PluginManager.d.ts

@@ -205,6 +205,7 @@ export default class PluginManager {
         '@jbrowse/core/util/layouts': typeof import("./util/layouts");
         '@jbrowse/core/util/tracks': typeof import("./util/tracks");
         '@jbrowse/core/util/Base1DViewModel': import("mobx-state-tree").IModelType<{
+            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
             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>;
@@ -228,6 +229,7 @@ export default class PluginManager {
             setVolatileWidth(width: number): void;
         } & {
             readonly width: number;
+            readonly assemblyNames: string[];
             readonly displayedRegionsTotalPx: number;
             readonly maxOffset: number;
             readonly minOffset: number;

package/ReExports/modules.d.ts

@@ -133,6 +133,7 @@ declare const libs: {
     '@jbrowse/core/util/layouts': typeof coreLayouts;
     '@jbrowse/core/util/tracks': typeof trackUtils;
     '@jbrowse/core/util/Base1DViewModel': mst.IModelType<{
+        id: mst.IOptionalIType<mst.ISimpleType<string>, [undefined]>;
         displayedRegions: mst.IArrayType<mst.IModelType<{
             refName: mst.ISimpleType<string>;
             start: mst.ISimpleType<number>;
@@ -156,6 +157,7 @@ declare const libs: {
         setVolatileWidth(width: number): void;
     } & {
         readonly width: number;
+        readonly assemblyNames: string[];
         readonly displayedRegionsTotalPx: number;
         readonly maxOffset: number;
         readonly minOffset: number;

package/TextSearch/TextSearchManager.d.ts

@@ -29,10 +29,10 @@ export default class TextSearchManager {
      */
     relevantAdapters(searchScope: SearchScope): (import("mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
         setSubschema(slotName: string, data: unknown): any;
-    } & import("mobx-state-tree").IStateTreeNode<import("../configuration/configurationSchema").AnyConfigurationSchemaType>)[];
+    } & import("mobx-state-tree").IStateTreeNode<import("../configuration").AnyConfigurationSchemaType>)[];
     getAdaptersWithAssembly(asmName: string, adapterConfs: AnyConfigurationModel[]): (import("mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
         setSubschema(slotName: string, data: unknown): any;
-    } & import("mobx-state-tree").IStateTreeNode<import("../configuration/configurationSchema").AnyConfigurationSchemaType>)[];
+    } & import("mobx-state-tree").IStateTreeNode<import("../configuration").AnyConfigurationSchemaType>)[];
     /**
      * Returns list of relevant results given a search query and options
      * @param args - search options/arguments include: search query

package/assemblyManager/assemblyConfigSchema.d.ts

@@ -1,3 +1,3 @@
 import PluginManager from '../PluginManager';
-declare const _default: (pluginManager: PluginManager) => import("../configuration/configurationSchema").AnyConfigurationSchemaType;
+declare const _default: (pluginManager: PluginManager) => import("../configuration").AnyConfigurationSchemaType;
 export default _default;

package/assemblyManager/assemblyManager.d.ts

@@ -169,7 +169,7 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
     readonly assemblyNamesList: string[];
     readonly assemblyList: (import("mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
         setSubschema(slotName: string, data: unknown): any;
-    } & import("mobx-state-tree").IStateTreeNode<import("../configuration/configurationSchema").AnyConfigurationSchemaType> & {
+    } & import("mobx-state-tree").IStateTreeNode<import("../configuration").AnyConfigurationSchemaType> & {
         name: string;
     })[];
     readonly rpcManager: any;

package/configuration/index.d.ts

@@ -1,3 +1,3 @@
 export { ConfigurationSchema, ConfigurationReference, } from './configurationSchema';
-export type { AnyConfigurationModel } from './configurationSchema';
+export type { AnyConfigurationModel, AnyConfigurationSchemaType, } from './configurationSchema';
 export * from './util';

package/data_adapters/BaseAdapter.d.ts

@@ -1,6 +1,6 @@
 import { Observable } from 'rxjs';
 import { Feature } from '../util/simpleFeature';
-import { AnyConfigurationModel } from '../configuration/configurationSchema';
+import { AnyConfigurationModel } from '../configuration';
 import { getSubAdapterType } from './dataAdapterCache';
 import { AugmentedRegion as Region, NoAssemblyRegion } from '../util/types';
 import BaseResult from '../TextSearch/BaseResults';
@@ -59,6 +59,7 @@ export declare abstract class BaseFeatureDataAdapter extends BaseAdapter {
      * @param opts - Feature adapter options
      */
     abstract getRefNames(opts?: BaseOptions): Promise<string[]>;
+    getConf(arg: string | string[]): any;
     /**
      * Get features from the data source that overlap a region
      * @param region - Region

package/data_adapters/BaseAdapter.js

@@ -40,7 +40,7 @@ var _rxjs2 = require("../util/rxjs");
 
 var _util = require("../util");
 
-var _configurationSchema = require("../configuration/configurationSchema");
+var _configuration = require("../configuration");
 
 var _stats = require("../util/stats");
 
@@ -55,7 +55,7 @@ function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflec
 function _isNativeReflectConstruct() { if (typeof Reflect === "undefined" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === "function") return true; try { Boolean.prototype.valueOf.call(Reflect.construct(Boolean, [], function () {})); return true; } catch (e) { return false; } }
 
 var BaseAdapter = /*#__PURE__*/(0, _createClass2.default)(function BaseAdapter() {
-  var config = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : (0, _configurationSchema.ConfigurationSchema)('empty', {}).create();
+  var config = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : (0, _configuration.ConfigurationSchema)('empty', {}).create();
   var getSubAdapter = arguments.length > 1 ? arguments[1] : undefined;
   var pluginManager = arguments.length > 2 ? arguments[2] : undefined;
   (0, _classCallCheck2.default)(this, BaseAdapter);
@@ -97,6 +97,24 @@ var BaseFeatureDataAdapter = /*#__PURE__*/function (_BaseAdapter) {
   }
 
   (0, _createClass2.default)(BaseFeatureDataAdapter, [{
+    key: "getConf",
+    value: // public abstract async getRefNames(opts?: BaseOptions): Promise<string[]>
+    //   await this.setup()
+    //   const { refNames } = this.metadata
+    //   return refNames
+    // }
+    //
+    function getConf(arg) {
+      return (0, _configuration.readConfObject)(this.config, arg);
+    }
+    /**
+     * Get features from the data source that overlap a region
+     * @param region - Region
+     * @param options - Feature adapter options
+     * @returns Observable of Feature objects in the region
+     */
+
+  }, {
     key: "getHeader",
     value: // public abstract getFeatures(
     //   region: Region,
@@ -436,6 +454,14 @@ var BaseFeatureDataAdapter = /*#__PURE__*/function (_BaseAdapter) {
           while (1) {
             switch (_context10.prev = _context10.next) {
               case 0:
+                if (regions.length) {
+                  _context10.next = 2;
+                  break;
+                }
+
+                throw new Error('No regions to estimate stats for');
+
+              case 2:
                 region = regions[0];
                 lastTime = +Date.now();
 
@@ -522,7 +548,7 @@ var BaseFeatureDataAdapter = /*#__PURE__*/function (_BaseAdapter) {
 
                 return _context10.abrupt("return", statsFromInterval(1000, 0));
 
-              case 5:
+              case 7:
               case "end":
                 return _context10.stop();
             }

package/data_adapters/CytobandAdapter.d.ts

@@ -1,6 +1,6 @@
 import SimpleFeature from '../util/simpleFeature';
 import { BaseAdapter } from './BaseAdapter';
-declare const configSchema: import("../configuration/configurationSchema").AnyConfigurationSchemaType;
+declare const configSchema: import("../configuration").AnyConfigurationSchemaType;
 declare class CytobandAdapter extends BaseAdapter {
     getData(): Promise<SimpleFeature[]>;
     freeResources(): void;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "1.6.4",
+  "version": "1.6.7",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
     "jbrowse",
@@ -26,12 +26,12 @@
     "clean": "rimraf dist",
     "prebuild": "yarn clean",
     "prepack": "yarn build",
-    "build": "NODE_ENV=production babel . --root-mode upward --out-dir dist --extensions '.ts,.js,.tsx,.jsx' && cp package.json README.md ../../LICENSE dist/ && tsc"
+    "build": "babel . --root-mode upward --out-dir dist --extensions '.ts,.js,.tsx,.jsx' && cp package.json README.md ../../LICENSE dist/ && tsc"
   },
   "dependencies": {
     "@babel/runtime": "^7.16.3",
     "@material-ui/icons": "^4.0.1",
-    "abortable-promise-cache": "^1.1.3",
+    "abortable-promise-cache": "^1.5.0",
     "base64-js": "^1.3.0",
     "canvas": "^2.8.0",
     "clsx": "^1.0.4",
@@ -77,5 +77,5 @@
     "access": "public",
     "directory": "dist"
   },
-  "gitHead": "7f157fbb2302d8825f99d01bcc0fd0616116c5d2"
+  "gitHead": "02012ec299c36647f755316571775d36b0fee5ec"
 }

package/pluggableElementTypes/RpcMethodType.js

@@ -245,7 +245,7 @@ var RpcMethodType = /*#__PURE__*/function (_PluggableElementBase) {
                 }
 
                 // @ts-ignore
-                retryAccount = rootModel === null || rootModel === void 0 ? void 0 : rootModel.createEphemeralInternetAccount("HTTPBasicInternetAccount-".concat(new URL(_context5.t0.location.uri).origin), {}, _context5.t0.location);
+                retryAccount = rootModel === null || rootModel === void 0 ? void 0 : rootModel.createEphemeralInternetAccount("HTTPBasicInternetAccount-".concat(new URL(_context5.t0.url).origin), {}, _context5.t0.url);
                 throw new _types.RetryError('Retrying with created internet account', retryAccount.internetAccountId);
 
               case 12:

package/pluggableElementTypes/models/InternetAccountModel.d.ts

@@ -1,24 +1,120 @@
 import React from 'react';
 import { Instance } from 'mobx-state-tree';
 import { RemoteFileWithRangeCache } from '../../util/io';
-import { FileLocation, UriLocation, AnyReactComponentType } from '../../util/types';
+import { UriLocation, AnyReactComponentType } from '../../util/types';
 export declare const InternetAccount: 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>;
 }, {
-    readonly name: any;
-    readonly internetAccountId: any;
-    readonly tokenType: any;
-    readonly accountConfig: any;
+    readonly name: string;
+    readonly description: string;
+    readonly internetAccountId: string;
+    readonly authHeader: string;
+    readonly tokenType: string;
+    readonly domains: string[];
+    /**
+     * Can use this to customize what is displayed in fileSelector's toggle box
+     */
     readonly toggleContents: React.ReactNode;
+    /**
+     * 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;
+    /**
+     * Can use this to add a label to the UrlChooser. Has no effect if a custom
+     * SelectorComponent is supplied
+     */
     readonly selectorLabel: string | undefined;
-    handlesLocation(location: FileLocation): boolean;
 } & {
-    openLocation(location: UriLocation): RemoteFileWithRangeCache;
+    /**
+     * Determine whether this internetAccount provides credentials for a URL
+     * @param location  - UriLocation of resource
+     * @returns true or false
+     */
+    handlesLocation(location: UriLocation): boolean;
+    /**
+     * The key used to store this internetAccount's token in sessionStorage
+     */
+    readonly tokenKey: string;
+} & {
+    /**
+     * 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;
+    storeToken(token: string): void;
+    removeToken(): void;
+    retrieveToken(): string | null;
+    /**
+     * 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 location - UriLocation of the resource
+     * @returns - Valid auth token
+     */
+    validateToken(token: string, location: UriLocation): Promise<string>;
+} & {
+    /**
+     * 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 | undefined): Promise<string>;
+} & {
+    addAuthHeaderToInit(init: RequestInit | undefined, token: string): {
+        headers: Headers;
+        body?: BodyInit | null | undefined;
+        cache?: RequestCache | undefined;
+        credentials?: RequestCredentials | undefined;
+        integrity?: string | undefined;
+        keepalive?: boolean | undefined;
+        method?: string | undefined;
+        mode?: RequestMode | undefined;
+        redirect?: RequestRedirect | undefined;
+        referrer?: string | undefined;
+        referrerPolicy?: ReferrerPolicy | undefined;
+        signal?: AbortSignal | null | undefined;
+        window?: null | undefined;
+    };
+    /**
+     * 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: {
+            token: string;
+            configuration: any;
+        };
     }>;
+} & {
+    /**
+     * 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 location - UriLocation of the resource
+     * @returns A function that can be used to fetch
+     */
+    getFetcher(location?: UriLocation | undefined): (input: RequestInfo, init?: RequestInit | undefined) => Promise<Response>;
+} & {
+    /**
+     * 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 declare type BaseInternetAccountStateModel = typeof InternetAccount;
 export declare type BaseInternetAccountModel = Instance<BaseInternetAccountStateModel>;