@jbrowse/core 1.6.5 → 1.6.6

package/util/io/index.js

@@ -11,12 +11,15 @@ Object.defineProperty(exports, "RemoteFileWithRangeCache", {
     return _RemoteFileWithRangeCache.RemoteFileWithRangeCache;
   }
 });
+exports.getFetcher = getFetcher;
 exports.openLocation = openLocation;
 
 var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
 
 var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
 
+var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
+
 var _genericFilehandle = require("generic-filehandle");
 
 var _RemoteFileWithRangeCache = require("./RemoteFileWithRangeCache");
@@ -27,6 +30,10 @@ var _tracks = require("../tracks");
 
 var _detectNode = _interopRequireDefault(require("detect-node"));
 
+function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }
+
+function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
+
 function isLocalPathLocation(location) {
   return 'localPath' in location;
 }
@@ -36,50 +43,6 @@ function isBlobLocation(location) {
 }
 
 function openLocation(location, pluginManager) {
-  function checkAuthNeededFetch(_x, _x2) {
-    return _checkAuthNeededFetch.apply(this, arguments);
-  }
-
-  function _checkAuthNeededFetch() {
-    _checkAuthNeededFetch = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(url, opts) {
-      var response, authHeaders;
-      return _regenerator.default.wrap(function _callee$(_context) {
-        while (1) {
-          switch (_context.prev = _context.next) {
-            case 0:
-              _context.next = 2;
-              return fetch(url, opts);
-
-            case 2:
-              response = _context.sent;
-
-              if (!(response.status === 401)) {
-                _context.next = 7;
-                break;
-              }
-
-              authHeaders = response.headers.get('WWW-Authenticate');
-
-              if (!((0, _types.isUriLocation)(location) && authHeaders && authHeaders.includes('Basic'))) {
-                _context.next = 7;
-                break;
-              }
-
-              throw new _types.AuthNeededError('Accessing HTTPBasic resource without authentication', location);
-
-            case 7:
-              return _context.abrupt("return", response);
-
-            case 8:
-            case "end":
-              return _context.stop();
-          }
-        }
-      }, _callee);
-    }));
-    return _checkAuthNeededFetch.apply(this, arguments);
-  }
-
   if (!location) {
     throw new Error('must provide a location to openLocation');
   }
@@ -108,66 +71,114 @@ function openLocation(location, pluginManager) {
   }
 
   if ((0, _types.isUriLocation)(location)) {
+    // Check for empty string
     if (!location.uri) {
       throw new Error('No URI provided');
-    }
+    } // Resolve any relative URLs to absolute URLs
 
-    if (location.internetAccountPreAuthorization) {
-      if (!pluginManager) {
-        throw new Error('need plugin manager to open locations with an internet account');
-      }
 
-      var rootModel = pluginManager.rootModel;
+    var absoluteLocation = location.baseUri ? _objectSpread(_objectSpread({}, location), {}, {
+      uri: new URL(location.uri, location.baseUri).href
+    }) : location; // If there is a plugin manager, we can try internet accounts
+
+    if (pluginManager) {
+      var internetAccount = getInternetAccount(location, pluginManager); // If an internetAccount was found, use it to open the location
 
-      if (rootModel && !(0, _types.isAppRootModel)(rootModel)) {
-        throw new Error('This context does not support internet accounts');
+      if (internetAccount) {
+        return internetAccount.openLocation(absoluteLocation);
       }
+    } // Otherwise fall back on usual open
 
-      var internetAccount;
 
-      if (rootModel) {
-        internetAccount = rootModel.findAppropriateInternetAccount(location);
-      } else {
-        var internetAccountType = pluginManager.getInternetAccountType(location.internetAccountPreAuthorization.internetAccountType);
-        internetAccount = internetAccountType.stateModel.create({
-          type: location.internetAccountPreAuthorization.internetAccountType,
-          configuration: location.internetAccountPreAuthorization.authInfo.configuration
-        });
+    return new _RemoteFileWithRangeCache.RemoteFileWithRangeCache(absoluteLocation.uri, {
+      fetch: checkAuthNeededFetch
+    });
+  }
 
-        if (!location.internetAccountPreAuthorization.authInfo.token) {
-          throw new Error('Failed to obtain token from internet account. Try reloading the page');
-        }
-      }
+  throw new Error('invalid fileLocation');
+}
 
-      if (!internetAccount) {
-        throw new Error('Could not find associated internet account');
-      }
+function getFetcher(location, pluginManager) {
+  if (!(0, _types.isUriLocation)(location)) {
+    throw new Error("Not a valid UriLocation: ".concat(JSON.stringify(location)));
+  }
 
-      return internetAccount.openLocation(location);
-    } else if (pluginManager) {
-      var _rootModel = pluginManager.rootModel;
+  var internetAccount = getInternetAccount(location, pluginManager);
 
-      if (_rootModel && (0, _types.isAppRootModel)(_rootModel)) {
-        var modifiedLocation = JSON.parse(JSON.stringify(location));
+  if (internetAccount) {
+    return internetAccount.getFetcher(location);
+  }
 
-        var _internetAccount = _rootModel.findAppropriateInternetAccount(location);
+  return checkAuthNeededFetch;
+}
 
-        if (_internetAccount) {
-          _internetAccount.getPreAuthorizationInformation(location).then( // eslint-disable-next-line @typescript-eslint/no-explicit-any
-          function (preAuthInfo) {
-            return modifiedLocation.internetAccountPreAuthorization = preAuthInfo;
-          });
+function getInternetAccount(location, pluginManager) {
+  var rootModel = pluginManager.rootModel; // If there is an appRootModel, use it to find the internetAccount
 
-          return _internetAccount.openLocation(modifiedLocation);
-        }
-      }
+  if (rootModel && (0, _types.isAppRootModel)(rootModel)) {
+    return rootModel.findAppropriateInternetAccount(location);
+  } // If there is no appRootModel, but there is pre-auth, create a temporary
+  // internetAccount. This is typical in a worker.
+
+
+  if (location.internetAccountPreAuthorization) {
+    if (!location.internetAccountPreAuthorization.authInfo.token) {
+      throw new Error('Failed to obtain token from internet account. Try reloading the page');
     }
 
-    var url = location.baseUri ? new URL(location.uri, location.baseUri).href : location.uri;
-    return new _RemoteFileWithRangeCache.RemoteFileWithRangeCache(url, {
-      fetch: checkAuthNeededFetch
+    var internetAccountType = pluginManager.getInternetAccountType(location.internetAccountPreAuthorization.internetAccountType);
+    return internetAccountType.stateModel.create({
+      type: location.internetAccountPreAuthorization.internetAccountType,
+      configuration: location.internetAccountPreAuthorization.authInfo.configuration
     });
   }
 
-  throw new Error('invalid fileLocation');
+  return;
+} // This fetch throws a special error if the response is "401" and includes a
+// "WWW-Authenticate: Basic" header. This is so downstream code can retry if
+// needed with HTTP Basic authentication included
+
+
+function checkAuthNeededFetch(_x, _x2) {
+  return _checkAuthNeededFetch.apply(this, arguments);
+}
+
+function _checkAuthNeededFetch() {
+  _checkAuthNeededFetch = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(url, opts) {
+    var response, authHeaders;
+    return _regenerator.default.wrap(function _callee$(_context) {
+      while (1) {
+        switch (_context.prev = _context.next) {
+          case 0:
+            _context.next = 2;
+            return fetch(url, opts);
+
+          case 2:
+            response = _context.sent;
+
+            if (!(response.status === 401)) {
+              _context.next = 7;
+              break;
+            }
+
+            authHeaders = response.headers.get('WWW-Authenticate');
+
+            if (!(authHeaders && authHeaders.includes('Basic'))) {
+              _context.next = 7;
+              break;
+            }
+
+            throw new _types.AuthNeededError('Accessing HTTPBasic resource without authentication', url.toString());
+
+          case 7:
+            return _context.abrupt("return", response);
+
+          case 8:
+          case "end":
+            return _context.stop();
+        }
+      }
+    }, _callee);
+  }));
+  return _checkAuthNeededFetch.apply(this, arguments);
 }

package/util/offscreenCanvasPonyfill.js

@@ -264,14 +264,14 @@ var PonyfillOffscreenContext = /*#__PURE__*/function () {
       var x = args[0],
           y = args[1],
           w = args[2],
-          h = args[3];
+          h = args[3]; // avoid rendering offscreen contents
 
       if (x > this.width || x + w < 0) {
         return;
       }
 
       var nx = Math.max(x, 0);
-      var nw = nx + w > this.width ? this.width - nx : w;
+      var nw = w - (nx - x);
       this.commands.push({
         type: 'fillRect',
         args: [nx, y, nw, h]

package/util/simpleFeature.d.ts

@@ -6,6 +6,9 @@ export interface Feature {
      * Get a piece of data about the feature.  All features must have
      * 'start' and 'end', but everything else is optional.
      */
+    get(name: 'refName'): string;
+    get(name: 'start'): number;
+    get(name: 'end'): number;
     get(name: string): any;
     /**
      * Set an item of data.

package/util/types/index.d.ts

@@ -186,8 +186,8 @@ export interface UriLocation extends SnapshotIn<typeof MUUriLocation> {
 export declare function isUriLocation(location: unknown): location is UriLocation;
 export declare class AuthNeededError extends Error {
     message: string;
-    location: UriLocation;
-    constructor(message: string, location: UriLocation);
+    url: string;
+    constructor(message: string, url: string);
 }
 export declare class RetryError extends Error {
     message: string;

package/util/types/index.js

@@ -158,13 +158,13 @@ var AuthNeededError = /*#__PURE__*/function (_Error) {
 
   var _super = _createSuper(AuthNeededError);
 
-  function AuthNeededError(message, location) {
+  function AuthNeededError(message, url) {
     var _this;
 
     (0, _classCallCheck2.default)(this, AuthNeededError);
     _this = _super.call(this, message);
     _this.message = message;
-    _this.location = location;
+    _this.url = url;
     _this.name = 'AuthNeededError';
     Object.setPrototypeOf((0, _assertThisInitialized2.default)(_this), AuthNeededError.prototype);
     return _this;
@@ -198,7 +198,7 @@ exports.RetryError = RetryError;
 
 function isAuthNeededException(exception) {
   return exception instanceof Error && ( // DOMException
-  exception.name === 'AuthNeededError' || exception.location !== undefined);
+  exception.name === 'AuthNeededError' || exception.url !== undefined);
 }
 
 function isRetryException(exception) {