@jbrowse/core 1.4.1 → 1.5.2

package/util/io/index.js

@@ -5,28 +5,27 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
+Object.defineProperty(exports, "RemoteFileWithRangeCache", {
+  enumerable: true,
+  get: function get() {
+    return _RemoteFileWithRangeCache.RemoteFileWithRangeCache;
+  }
+});
 exports.openLocation = openLocation;
-exports.openUrl = void 0;
-
-var _genericFilehandle = require("generic-filehandle");
 
-var _LocalFile = _interopRequireDefault(require("./LocalFile"));
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
 
-var _rangeFetcher = require("./rangeFetcher");
+var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
 
-var _tracks = require("../tracks");
+var _genericFilehandle = require("generic-filehandle");
 
-var _util = require("../../util");
+var _RemoteFileWithRangeCache = require("./RemoteFileWithRangeCache");
 
-var openUrl = function openUrl(arg) {
-  return (0, _rangeFetcher.openUrl)(arg);
-};
+var _types = require("../types");
 
-exports.openUrl = openUrl;
+var _tracks = require("../tracks");
 
-function isUriLocation(location) {
-  return 'uri' in location;
-}
+var _detectNode = _interopRequireDefault(require("detect-node"));
 
 function isLocalPathLocation(location) {
   return 'localPath' in location;
@@ -36,7 +35,51 @@ function isBlobLocation(location) {
   return 'blobId' in location;
 }
 
-function openLocation(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');
   }
@@ -46,21 +89,13 @@ function openLocation(location) {
       throw new Error('No local path provided');
     }
 
-    if (_util.isElectron || typeof jest !== 'undefined') {
-      return new _LocalFile.default(location.localPath);
+    if (_detectNode.default) {
+      return new _genericFilehandle.LocalFile(location.localPath);
     } else {
       throw new Error("can't use local files in the browser");
     }
   }
 
-  if (isUriLocation(location)) {
-    if (!location.uri) {
-      throw new Error('No URI provided');
-    }
-
-    return openUrl(location.baseUri ? new URL(location.uri, location.baseUri).href : location.uri);
-  }
-
   if (isBlobLocation(location)) {
     // special case where blob is not directly stored on the model, use a getter
     var blob = (0, _tracks.getBlob)(location.blobId);
@@ -72,5 +107,79 @@ function openLocation(location) {
     return new _genericFilehandle.BlobFile(blob);
   }
 
+  if ((0, _types.isUriLocation)(location)) {
+    if (!location.uri) {
+      throw new Error('No URI provided');
+    }
+
+    if (location.internetAccountPreAuthorization) {
+      if (!pluginManager) {
+        throw new Error('need plugin manager to open locations with an internet account');
+      }
+
+      var rootModel = pluginManager.rootModel;
+
+      if (rootModel && !(0, _types.isAppRootModel)(rootModel)) {
+        throw new Error('This context does not support internet accounts');
+      }
+
+      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
+        });
+
+        if (!location.internetAccountPreAuthorization.authInfo.token) {
+          throw new Error('Failed to obtain token from internet account. Try reloading the page');
+        }
+      }
+
+      if (!internetAccount) {
+        throw new Error('Could not find associated internet account');
+      }
+
+      return internetAccount.openLocation(location);
+    } else if (location.internetAccountId) {
+      if (!pluginManager) {
+        throw new Error('need plugin manager to open locations with an internet account');
+      }
+
+      var _rootModel = pluginManager.rootModel;
+
+      if (_rootModel && !(0, _types.isAppRootModel)(_rootModel)) {
+        throw new Error('This context does not support internet accounts');
+      }
+
+      if (_rootModel) {
+        var modifiedLocation = JSON.parse(JSON.stringify(location));
+
+        var _internetAccount = _rootModel.findAppropriateInternetAccount(location);
+
+        if (!_internetAccount) {
+          throw new Error('Could not find associated internet account');
+        }
+
+        _internetAccount.getPreAuthorizationInformation(location).then( // eslint-disable-next-line @typescript-eslint/no-explicit-any
+        function (preAuthInfo) {
+          return modifiedLocation.internetAccountPreAuthorization = preAuthInfo;
+        });
+
+        return _internetAccount.openLocation(modifiedLocation);
+      }
+
+      throw new Error('Could not pre-authorize location');
+    }
+
+    var url = location.baseUri ? new URL(location.uri, location.baseUri).href : location.uri;
+    return new _RemoteFileWithRangeCache.RemoteFileWithRangeCache(url, {
+      fetch: checkAuthNeededFetch
+    });
+  }
+
   throw new Error('invalid fileLocation');
 }

package/util/jexl.js

@@ -9,7 +9,9 @@ exports.default = _default;
 
 var _jexl = _interopRequireDefault(require("jexl"));
 
-function _default() {
+function
+  /* config?: any*/
+_default() {
   var j = new _jexl.default.Jexl(); // someday will make sure all of configs callbacks are added in, including
   // ones passed in
   // below are core functions
@@ -40,6 +42,7 @@ function _default() {
   j.addFunction('floor', Math.floor);
   j.addFunction('round', Math.round);
   j.addFunction('abs', Math.abs);
+  j.addFunction('log10', Math.log10);
   j.addFunction('parseInt', Number.parseInt);
   j.addFunction('parseFloat', Number.parseFloat); // string
 

package/util/layouts/BaseLayout.d.ts

@@ -10,11 +10,14 @@ export interface Rectangle<T> {
     r: number;
     top: number | null;
     h: number;
+    originalHeight: number;
     data?: Record<string, T>;
 }
 export interface BaseLayout<T> {
     addRect(id: string, left: number, right: number, height: number, data?: Record<string, T>): number | null;
     collides(rect: Rectangle<T>, top: number): boolean;
+    addRectToBitmap(rect: Rectangle<T>, data: Record<string, T>): void;
+    getRectangles(): Map<string, RectTuple>;
     discardRange(left: number, right: number): void;
     serializeRegion(region: {
         start: number;

package/util/layouts/GranularRectLayout.d.ts

@@ -1,38 +1,47 @@
-import { RectTuple, SerializedLayout, BaseLayout } from './BaseLayout';
+import { RectTuple, SerializedLayout, Rectangle, BaseLayout } from './BaseLayout';
 export default class GranularRectLayout<T> implements BaseLayout<T> {
+    private pitchX;
+    private pitchY;
+    private hardRowLimit;
+    private bitmap;
     private rectangles;
     maxHeightReached: boolean;
     private maxHeight;
-    private rbush;
-    private spacing;
+    private displayMode;
     private pTotalHeight;
-    private pitchX;
-    constructor({ maxHeight, spacing, pitchX, }?: {
-        maxHeight?: number;
-        spacing?: number;
+    constructor({ pitchX, pitchY, maxHeight, hardRowLimit, displayMode, }?: {
         pitchX?: number;
+        pitchY?: number;
+        maxHeight?: number;
+        displayMode?: string;
+        hardRowLimit?: number;
     });
     /**
      * @returns top position for the rect, or Null if laying
      *  out the rect would exceed maxHeight
      */
     addRect(id: string, left: number, right: number, height: number, data?: Record<string, T>): number | null;
-    collides(): boolean;
+    collides(rect: Rectangle<T>, top: number): boolean;
+    /**
+     * make a subarray if it does not exist
+     */
+    private autovivifyRow;
+    addRectToBitmap(rect: Rectangle<T>): void;
     /**
      *  Given a range of X coordinates, deletes all data dealing with
      *  the features.
      */
-    discardRange(): void;
+    discardRange(left: number, right: number): void;
     hasSeen(id: string): boolean;
     getByCoord(x: number, y: number): Record<string, T> | string | undefined;
     getByID(id: string): RectTuple | undefined;
     cleanup(): void;
     getTotalHeight(): number;
     get totalHeight(): number;
+    getRectangles(): Map<string, RectTuple>;
     serializeRegion(region: {
         start: number;
         end: number;
     }): SerializedLayout;
-    getRectangles(): Map<string, RectTuple>;
     toJSON(): SerializedLayout;
 }