@jbrowse/core 1.6.5 → 1.6.8

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,
@@ -197,7 +215,7 @@ var BaseFeatureDataAdapter = /*#__PURE__*/function (_BaseAdapter) {
                   if (!hasData) {
                     observer.complete();
                   } else {
-                    _this.getFeatures(region, opts).pipe((0, _operators.takeUntil)((0, _util.observeAbortSignal)(opts.signal))).subscribe(observer);
+                    _this.getFeatures(region, opts).subscribe(observer);
                   }
 
                 case 5:
@@ -235,47 +253,9 @@ var BaseFeatureDataAdapter = /*#__PURE__*/function (_BaseAdapter) {
       var _this2 = this;
 
       var opts = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {};
-
-      var obs = _rxjs.merge.apply(void 0, (0, _toConsumableArray2.default)(regions.map(function (region) {
-        return (0, _rxjs2.ObservableCreate)( /*#__PURE__*/function () {
-          var _ref2 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4(observer) {
-            var hasData;
-            return _regenerator.default.wrap(function _callee4$(_context4) {
-              while (1) {
-                switch (_context4.prev = _context4.next) {
-                  case 0:
-                    _context4.next = 2;
-                    return _this2.hasDataForRefName(region.refName, opts);
-
-                  case 2:
-                    hasData = _context4.sent;
-                    (0, _util.checkAbortSignal)(opts.signal);
-
-                    if (!hasData) {
-                      observer.complete();
-                    } else {
-                      _this2.getFeatures(region, opts).subscribe(observer);
-                    }
-
-                  case 5:
-                  case "end":
-                    return _context4.stop();
-                }
-              }
-            }, _callee4);
-          }));
-
-          return function (_x4) {
-            return _ref2.apply(this, arguments);
-          };
-        }());
+      return _rxjs.merge.apply(void 0, (0, _toConsumableArray2.default)(regions.map(function (region) {
+        return _this2.getFeaturesInRegion(region, opts);
       })));
-
-      if (opts.signal) {
-        return obs.pipe((0, _operators.takeUntil)((0, _util.observeAbortSignal)(opts.signal)));
-      }
-
-      return obs;
     }
     /**
      * Check if the store has data for the given reference name.
@@ -286,31 +266,31 @@ var BaseFeatureDataAdapter = /*#__PURE__*/function (_BaseAdapter) {
   }, {
     key: "hasDataForRefName",
     value: function () {
-      var _hasDataForRefName = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee5(refName) {
+      var _hasDataForRefName = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4(refName) {
         var opts,
             refNames,
-            _args5 = arguments;
-        return _regenerator.default.wrap(function _callee5$(_context5) {
+            _args4 = arguments;
+        return _regenerator.default.wrap(function _callee4$(_context4) {
           while (1) {
-            switch (_context5.prev = _context5.next) {
+            switch (_context4.prev = _context4.next) {
               case 0:
-                opts = _args5.length > 1 && _args5[1] !== undefined ? _args5[1] : {};
-                _context5.next = 3;
+                opts = _args4.length > 1 && _args4[1] !== undefined ? _args4[1] : {};
+                _context4.next = 3;
                 return this.getRefNames(opts);
 
               case 3:
-                refNames = _context5.sent;
-                return _context5.abrupt("return", refNames.includes(refName));
+                refNames = _context4.sent;
+                return _context4.abrupt("return", refNames.includes(refName));
 
               case 5:
               case "end":
-                return _context5.stop();
+                return _context4.stop();
             }
           }
-        }, _callee5, this);
+        }, _callee4, this);
       }));
 
-      function hasDataForRefName(_x5) {
+      function hasDataForRefName(_x4) {
         return _hasDataForRefName.apply(this, arguments);
       }
 
@@ -319,24 +299,24 @@ var BaseFeatureDataAdapter = /*#__PURE__*/function (_BaseAdapter) {
   }, {
     key: "getRegionStats",
     value: function () {
-      var _getRegionStats = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee6(region, opts) {
+      var _getRegionStats = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee5(region, opts) {
         var feats;
-        return _regenerator.default.wrap(function _callee6$(_context6) {
+        return _regenerator.default.wrap(function _callee5$(_context5) {
           while (1) {
-            switch (_context6.prev = _context6.next) {
+            switch (_context5.prev = _context5.next) {
               case 0:
                 feats = this.getFeatures(region, opts);
-                return _context6.abrupt("return", (0, _stats.scoresToStats)(region, feats));
+                return _context5.abrupt("return", (0, _stats.scoresToStats)(region, feats));
 
               case 2:
               case "end":
-                return _context6.stop();
+                return _context5.stop();
             }
           }
-        }, _callee6, this);
+        }, _callee5, this);
       }));
 
-      function getRegionStats(_x6, _x7) {
+      function getRegionStats(_x5, _x6) {
         return _getRegionStats.apply(this, arguments);
       }
 
@@ -345,7 +325,7 @@ var BaseFeatureDataAdapter = /*#__PURE__*/function (_BaseAdapter) {
   }, {
     key: "getMultiRegionStats",
     value: function () {
-      var _getMultiRegionStats = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee7() {
+      var _getMultiRegionStats = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee6() {
         var _this3 = this;
 
         var regions,
@@ -357,29 +337,29 @@ var BaseFeatureDataAdapter = /*#__PURE__*/function (_BaseAdapter) {
             scoreSumSquares,
             featureCount,
             basesCovered,
-            _args7 = arguments;
-        return _regenerator.default.wrap(function _callee7$(_context7) {
+            _args6 = arguments;
+        return _regenerator.default.wrap(function _callee6$(_context6) {
           while (1) {
-            switch (_context7.prev = _context7.next) {
+            switch (_context6.prev = _context6.next) {
               case 0:
-                regions = _args7.length > 0 && _args7[0] !== undefined ? _args7[0] : [];
-                opts = _args7.length > 1 ? _args7[1] : undefined;
+                regions = _args6.length > 0 && _args6[0] !== undefined ? _args6[0] : [];
+                opts = _args6.length > 1 ? _args6[1] : undefined;
 
                 if (regions.length) {
-                  _context7.next = 4;
+                  _context6.next = 4;
                   break;
                 }
 
-                return _context7.abrupt("return", (0, _stats.blankStats)());
+                return _context6.abrupt("return", (0, _stats.blankStats)());
 
               case 4:
-                _context7.next = 6;
+                _context6.next = 6;
                 return Promise.all(regions.map(function (region) {
                   return _this3.getRegionStats(region, opts);
                 }));
 
               case 6:
-                feats = _context7.sent;
+                feats = _context6.sent;
                 scoreMax = feats.map(function (a) {
                   return a.scoreMax;
                 }).reduce(function (a, b) {
@@ -402,7 +382,7 @@ var BaseFeatureDataAdapter = /*#__PURE__*/function (_BaseAdapter) {
                 basesCovered = feats.reduce(function (a, b) {
                   return a + b.basesCovered;
                 }, 0);
-                return _context7.abrupt("return", (0, _stats.rectifyStats)({
+                return _context6.abrupt("return", (0, _stats.rectifyStats)({
                   scoreMin: scoreMin,
                   scoreMax: scoreMax,
                   featureCount: featureCount,
@@ -413,10 +393,10 @@ var BaseFeatureDataAdapter = /*#__PURE__*/function (_BaseAdapter) {
 
               case 14:
               case "end":
-                return _context7.stop();
+                return _context6.stop();
             }
           }
-        }, _callee7);
+        }, _callee6);
       }));
 
       function getMultiRegionStats() {
@@ -428,16 +408,16 @@ var BaseFeatureDataAdapter = /*#__PURE__*/function (_BaseAdapter) {
   }, {
     key: "estimateRegionsStats",
     value: function () {
-      var _estimateRegionsStats = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee10(regions, opts) {
+      var _estimateRegionsStats = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee9(regions, opts) {
         var _this4 = this;
 
         var region, lastTime, statsFromInterval, maybeRecordStats;
-        return _regenerator.default.wrap(function _callee10$(_context10) {
+        return _regenerator.default.wrap(function _callee9$(_context9) {
           while (1) {
-            switch (_context10.prev = _context10.next) {
+            switch (_context9.prev = _context9.next) {
               case 0:
                 if (regions.length) {
-                  _context10.next = 2;
+                  _context9.next = 2;
                   break;
                 }
 
@@ -448,11 +428,11 @@ var BaseFeatureDataAdapter = /*#__PURE__*/function (_BaseAdapter) {
                 lastTime = +Date.now();
 
                 statsFromInterval = /*#__PURE__*/function () {
-                  var _ref3 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee8(length, expansionTime) {
+                  var _ref2 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee7(length, expansionTime) {
                     var start, end, sampleCenter, query, features;
-                    return _regenerator.default.wrap(function _callee8$(_context8) {
+                    return _regenerator.default.wrap(function _callee7$(_context7) {
                       while (1) {
-                        switch (_context8.prev = _context8.next) {
+                        switch (_context7.prev = _context7.next) {
                           case 0:
                             start = region.start, end = region.end;
                             sampleCenter = start * 0.75 + end * 0.25;
@@ -460,85 +440,85 @@ var BaseFeatureDataAdapter = /*#__PURE__*/function (_BaseAdapter) {
                               start: Math.max(0, Math.round(sampleCenter - length / 2)),
                               end: Math.min(Math.round(sampleCenter + length / 2), end)
                             });
-                            _context8.next = 5;
+                            _context7.next = 5;
                             return _this4.getFeatures(query, opts).pipe((0, _operators.toArray)()).toPromise();
 
                           case 5:
-                            features = _context8.sent;
-                            return _context8.abrupt("return", maybeRecordStats(length, {
+                            features = _context7.sent;
+                            return _context7.abrupt("return", maybeRecordStats(length, {
                               featureDensity: features.length / length
                             }, features.length, expansionTime));
 
                           case 7:
                           case "end":
-                            return _context8.stop();
+                            return _context7.stop();
                         }
                       }
-                    }, _callee8);
+                    }, _callee7);
                   }));
 
-                  return function statsFromInterval(_x10, _x11) {
-                    return _ref3.apply(this, arguments);
+                  return function statsFromInterval(_x9, _x10) {
+                    return _ref2.apply(this, arguments);
                   };
                 }();
 
                 maybeRecordStats = /*#__PURE__*/function () {
-                  var _ref4 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee9(interval, stats, statsSampleFeatures, expansionTime) {
+                  var _ref3 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee8(interval, stats, statsSampleFeatures, expansionTime) {
                     var refLen, currTime;
-                    return _regenerator.default.wrap(function _callee9$(_context9) {
+                    return _regenerator.default.wrap(function _callee8$(_context8) {
                       while (1) {
-                        switch (_context9.prev = _context9.next) {
+                        switch (_context8.prev = _context8.next) {
                           case 0:
                             refLen = region.end - region.start;
 
                             if (!(statsSampleFeatures >= 70 || interval * 2 > refLen)) {
-                              _context9.next = 5;
+                              _context8.next = 5;
                               break;
                             }
 
-                            return _context9.abrupt("return", stats);
+                            return _context8.abrupt("return", stats);
 
                           case 5:
                             if (!(expansionTime <= 5000)) {
-                              _context9.next = 12;
+                              _context8.next = 12;
                               break;
                             }
 
                             currTime = +Date.now();
                             expansionTime += currTime - lastTime;
                             lastTime = currTime;
-                            return _context9.abrupt("return", statsFromInterval(interval * 2, expansionTime));
+                            return _context8.abrupt("return", statsFromInterval(interval * 2, expansionTime));
 
                           case 12:
                             console.warn("Stats estimation reached timeout, or didn't get enough features");
-                            return _context9.abrupt("return", {
+                            return _context8.abrupt("return", {
                               featureDensity: Infinity
                             });
 
                           case 14:
                           case "end":
-                            return _context9.stop();
+                            return _context8.stop();
                         }
                       }
-                    }, _callee9);
+                    }, _callee8);
                   }));
 
-                  return function maybeRecordStats(_x12, _x13, _x14, _x15) {
-                    return _ref4.apply(this, arguments);
+                  return function maybeRecordStats(_x11, _x12, _x13, _x14) {
+                    return _ref3.apply(this, arguments);
                   };
                 }();
 
-                return _context10.abrupt("return", statsFromInterval(1000, 0));
+                return _context9.abrupt("return", statsFromInterval(1000, 0));
 
               case 7:
               case "end":
-                return _context10.stop();
+                return _context9.stop();
             }
           }
-        }, _callee10);
+        }, _callee9);
       }));
 
-      function estimateRegionsStats(_x8, _x9) {
+      function estimateRegionsStats(_x7, _x8) {
         return _estimateRegionsStats.apply(this, arguments);
       }
 
@@ -563,21 +543,21 @@ var BaseSequenceAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   (0, _createClass2.default)(BaseSequenceAdapter, [{
     key: "estimateRegionsStats",
     value: function () {
-      var _estimateRegionsStats2 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee11() {
-        return _regenerator.default.wrap(function _callee11$(_context11) {
+      var _estimateRegionsStats2 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee10() {
+        return _regenerator.default.wrap(function _callee10$(_context10) {
           while (1) {
-            switch (_context11.prev = _context11.next) {
+            switch (_context10.prev = _context10.next) {
               case 0:
-                return _context11.abrupt("return", {
+                return _context10.abrupt("return", {
                   featureDensity: 0
                 });
 
               case 1:
               case "end":
-                return _context11.stop();
+                return _context10.stop();
             }
           }
-        }, _callee11);
+        }, _callee10);
       }));
 
       function estimateRegionsStats() {

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": "1.6.5",
+  "version": "1.6.8",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
     "jbrowse",
@@ -77,5 +77,5 @@
     "access": "public",
     "directory": "dist"
   },
-  "gitHead": "ab41f017840ffef09f5d60b008281cedaa5abe26"
+  "gitHead": "585e522096651ef4afb188366bb46d723439dc1b"
 }

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>;