@jbrowse/plugin-grid-bookmark 1.6.9 → 1.7.3

package/dist/GridBookmarkWidget/model.js

@@ -0,0 +1,70 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = f;
+
+var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
+
+var _mobxStateTree = require("mobx-state-tree");
+
+var _mst = require("@jbrowse/core/util/types/mst");
+
+var LabeledRegionModel = _mobxStateTree.types.compose(_mst.Region, _mobxStateTree.types.model('Label', {
+  label: _mobxStateTree.types.optional(_mobxStateTree.types.string, '')
+})).actions(function (self) {
+  return {
+    setLabel: function setLabel(label) {
+      self.label = label;
+    }
+  };
+});
+
+function f(pluginManager) {
+  return _mobxStateTree.types.model('GridBookmarkModel', {
+    id: _mst.ElementId,
+    type: _mobxStateTree.types.literal('GridBookmarkWidget'),
+    view: _mobxStateTree.types.safeReference(pluginManager.pluggableMstType('view', 'stateModel')),
+    bookmarkedRegions: _mobxStateTree.types.array(LabeledRegionModel),
+    modelSelectedAssembly: ''
+  }).actions(function (self) {
+    return {
+      importBookmarks: function importBookmarks(regions) {
+        self.bookmarkedRegions = (0, _mobxStateTree.cast)(self.bookmarkedRegions.concat(regions));
+      },
+      addBookmark: function addBookmark(region) {
+        self.bookmarkedRegions.push(region);
+      },
+      removeBookmark: function removeBookmark(index) {
+        self.bookmarkedRegions.splice(index, 1);
+      },
+      clearAllBookmarks: function clearAllBookmarks() {
+        self.bookmarkedRegions.clear();
+      },
+      updateBookmarkLabel: function updateBookmarkLabel(index, label) {
+        var _self$bookmarkedRegio;
+
+        (_self$bookmarkedRegio = self.bookmarkedRegions[index]) === null || _self$bookmarkedRegio === void 0 ? void 0 : _self$bookmarkedRegio.setLabel(label);
+      },
+      setSelectedAssembly: function setSelectedAssembly(assembly) {
+        self.modelSelectedAssembly = assembly;
+      }
+    };
+  }).views(function (self) {
+    return {
+      get selectedAssembly() {
+        return self.modelSelectedAssembly || (self.bookmarkedRegions.length ? self.bookmarkedRegions[0].assemblyName : '');
+      },
+
+      get assemblies() {
+        return (0, _toConsumableArray2["default"])(new Set(self.bookmarkedRegions.map(function (region) {
+          return region.assemblyName;
+        })));
+      }
+
+    };
+  });
+}

package/dist/GridBookmarkWidget/types.d.ts

@@ -1,8 +1,7 @@
-import { AbstractViewModel } from '@jbrowse/core/util/types';
-import { Region } from '@jbrowse/core/util/types';
-export interface NavigableViewModel extends AbstractViewModel {
-    navToLocString: Function;
-}
-export interface LabeledRegion extends Region {
-    label: string;
-}
+import { AbstractViewModel, Region } from '@jbrowse/core/util/types';
+export interface NavigableViewModel extends AbstractViewModel {
+    navToLocString: Function;
+}
+export interface LabeledRegion extends Region {
+    label: string;
+}

package/dist/GridBookmarkWidget/types.js

@@ -0,0 +1,5 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});

package/dist/GridBookmarkWidget/utils.d.ts

@@ -1,5 +1,5 @@
-import { AbstractViewModel } from '@jbrowse/core/util/types';
-import { GridBookmarkModel } from './model';
-import { LabeledRegion } from './types';
-export declare function navToBookmark(locString: string, views: AbstractViewModel[], model: GridBookmarkModel): Promise<void>;
-export declare function downloadBookmarkFile(bookmarkedRegions: LabeledRegion[], fileFormat: string, model: GridBookmarkModel): void;
+import { AbstractViewModel } from '@jbrowse/core/util/types';
+import { GridBookmarkModel } from './model';
+import { LabeledRegion } from './types';
+export declare function navToBookmark(locString: string, views: AbstractViewModel[], model: GridBookmarkModel): Promise<void>;
+export declare function downloadBookmarkFile(bookmarkedRegions: LabeledRegion[], fileFormat: string, model: GridBookmarkModel): void;

package/dist/GridBookmarkWidget/utils.js

@@ -0,0 +1,136 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.downloadBookmarkFile = downloadBookmarkFile;
+exports.navToBookmark = navToBookmark;
+
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+
+var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
+
+var _fileSaver = require("file-saver");
+
+var _util = require("@jbrowse/core/util");
+
+function navToBookmark(_x, _x2, _x3) {
+  return _navToBookmark.apply(this, arguments);
+}
+
+function _navToBookmark() {
+  _navToBookmark = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee(locString, views, model) {
+    var selectedAssembly, lgv, session, assemblyManager, assembly, loc, refName, regions, canonicalRefName, newDisplayedRegion, view;
+    return _regenerator["default"].wrap(function _callee$(_context) {
+      while (1) {
+        switch (_context.prev = _context.next) {
+          case 0:
+            selectedAssembly = model.selectedAssembly;
+            lgv = views.find(function (view) {
+              return view.type === 'LinearGenomeView' && // @ts-ignore
+              view.assemblyNames[0] === selectedAssembly;
+            });
+
+            if (!lgv) {
+              _context.next = 6;
+              break;
+            }
+
+            lgv.navToLocString(locString);
+            _context.next = 28;
+            break;
+
+          case 6:
+            session = (0, _util.getSession)(model);
+            assemblyManager = session.assemblyManager;
+            _context.next = 10;
+            return assemblyManager.waitForAssembly(selectedAssembly);
+
+          case 10:
+            assembly = _context.sent;
+
+            if (!assembly) {
+              _context.next = 28;
+              break;
+            }
+
+            _context.prev = 12;
+            loc = (0, _util.parseLocString)(locString, function (refName) {
+              return session.assemblyManager.isValidRefName(refName, selectedAssembly);
+            });
+            refName = loc.refName;
+            regions = assembly.regions;
+            canonicalRefName = assembly.getCanonicalRefName(refName);
+
+            if (regions) {
+              newDisplayedRegion = regions.find(function (region) {
+                return region.refName === canonicalRefName;
+              });
+            }
+
+            view = session.addView('LinearGenomeView', {
+              displayName: selectedAssembly
+            });
+            _context.next = 21;
+            return (0, _util.when)(function () {
+              return view.initialized;
+            });
+
+          case 21:
+            view.setDisplayedRegions([JSON.parse(JSON.stringify(newDisplayedRegion))]);
+            view.navToLocString(locString);
+            _context.next = 28;
+            break;
+
+          case 25:
+            _context.prev = 25;
+            _context.t0 = _context["catch"](12);
+            session.notify("".concat(_context.t0), 'error');
+
+          case 28:
+          case "end":
+            return _context.stop();
+        }
+      }
+    }, _callee, null, [[12, 25]]);
+  }));
+  return _navToBookmark.apply(this, arguments);
+}
+
+function downloadBookmarkFile(bookmarkedRegions, fileFormat, model) {
+  var selectedAssembly = model.selectedAssembly;
+  var fileHeader = fileFormat === 'TSV' ? 'chrom\tstart\tend\tlabel\tassembly_name\tcoord_range\n' : '';
+  var fileContents = bookmarkedRegions.map(function (b) {
+    var label = b.label;
+    var labelVal = label === '' ? '.' : label;
+    var locString = (0, _util.assembleLocString)(b);
+
+    if (fileFormat === 'BED') {
+      if (b.assemblyName === selectedAssembly || selectedAssembly === 'all') {
+        // the "name" column (column 4) in a BED has a max of 255 characters
+        // according to the new spec: https://github.com/samtools/hts-specs/pull/570
+        return "".concat(b.refName, "\t").concat(b.start, "\t").concat(b.end, "\t").concat(labelVal.slice(0, 255), "\n");
+      }
+
+      return '';
+    } else {
+      return "".concat(b.refName, "\t").concat(b.start + 1, "\t").concat(b.end, "\t").concat(labelVal, "\t").concat(b.assemblyName, "\t").concat(locString, "\n");
+    }
+  }).reduce(function (a, b) {
+    return a + b;
+  }, fileHeader);
+  var blob = new Blob([fileContents || ''], {
+    type: fileFormat === 'BED' ? 'text/x-bed;charset=utf-8' : 'text/tab-separated-values;charset=utf-8'
+  });
+  var fileName;
+
+  if (fileFormat === 'BED') {
+    fileName = "jbrowse_bookmarks_".concat(selectedAssembly, ".bed");
+  } else {
+    fileName = 'jbrowse_bookmarks.tsv';
+  }
+
+  (0, _fileSaver.saveAs)(blob, fileName);
+}

package/dist/index.d.ts

@@ -1,7 +1,7 @@
-import Plugin from '@jbrowse/core/Plugin';
-import PluginManager from '@jbrowse/core/PluginManager';
-export default class extends Plugin {
-    name: string;
-    install(pluginManager: PluginManager): void;
-    configure(_pluginManager: PluginManager): void;
-}
+import Plugin from '@jbrowse/core/Plugin';
+import PluginManager from '@jbrowse/core/PluginManager';
+export default class extends Plugin {
+    name: string;
+    install(pluginManager: PluginManager): void;
+    configure(_pluginManager: PluginManager): void;
+}

package/dist/index.js

@@ -1,8 +1,192 @@
+"use strict";
 
-'use strict'
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
 
-if (process.env.NODE_ENV === 'production') {
-  module.exports = require('./plugin-grid-bookmark.cjs.production.min.js')
-} else {
-  module.exports = require('./plugin-grid-bookmark.cjs.development.js')
-}
+var _typeof = require("@babel/runtime/helpers/typeof");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
+
+var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
+
+var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
+
+var _assertThisInitialized2 = _interopRequireDefault(require("@babel/runtime/helpers/assertThisInitialized"));
+
+var _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));
+
+var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime/helpers/possibleConstructorReturn"));
+
+var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));
+
+var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
+
+var _react = require("react");
+
+var _Bookmark = _interopRequireDefault(require("@material-ui/icons/Bookmark"));
+
+var _Bookmarks = _interopRequireDefault(require("@material-ui/icons/Bookmarks"));
+
+var _WidgetType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/WidgetType"));
+
+var _Plugin2 = _interopRequireDefault(require("@jbrowse/core/Plugin"));
+
+var _util = require("@jbrowse/core/util");
+
+var _GridBookmarkWidget = require("./GridBookmarkWidget");
+
+function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
+
+function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { "default": obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj["default"] = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
+
+function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = (0, _getPrototypeOf2["default"])(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = (0, _getPrototypeOf2["default"])(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return (0, _possibleConstructorReturn2["default"])(this, result); }; }
+
+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 _default = /*#__PURE__*/function (_Plugin) {
+  (0, _inherits2["default"])(_default, _Plugin);
+
+  var _super = _createSuper(_default);
+
+  function _default() {
+    var _this;
+
+    (0, _classCallCheck2["default"])(this, _default);
+
+    for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
+      args[_key] = arguments[_key];
+    }
+
+    _this = _super.call.apply(_super, [this].concat(args));
+    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "name", 'GridBookmarkPlugin');
+    return _this;
+  }
+
+  (0, _createClass2["default"])(_default, [{
+    key: "install",
+    value: function install(pluginManager) {
+      pluginManager.addWidgetType(function () {
+        return new _WidgetType["default"]({
+          name: 'GridBookmarkWidget',
+          heading: 'Bookmarked regions',
+          configSchema: _GridBookmarkWidget.configSchema,
+          stateModel: (0, _GridBookmarkWidget.stateModelFactory)(pluginManager),
+          ReactComponent: /*#__PURE__*/(0, _react.lazy)(function () {
+            return Promise.resolve().then(function () {
+              return _interopRequireWildcard(require('./GridBookmarkWidget/components/GridBookmarkWidget'));
+            });
+          })
+        });
+      });
+      pluginManager.addToExtensionPoint('Core-extendPluggableElement', function (pluggableElement) {
+        if (pluggableElement.name === 'LinearGenomeView') {
+          var _ref = pluggableElement,
+              stateModel = _ref.stateModel;
+          var newStateModel = stateModel.extend(function (self) {
+            var superMenuItems = self.menuItems;
+            var superRubberBandMenuItems = self.rubberBandMenuItems;
+            return {
+              actions: {
+                activateBookmarkWidget: function activateBookmarkWidget() {
+                  var session = (0, _util.getSession)(self);
+
+                  if ((0, _util.isSessionModelWithWidgets)(session)) {
+                    var bookmarkWidget = session.widgets.get('GridBookmark');
+
+                    if (!bookmarkWidget) {
+                      bookmarkWidget = session.addWidget('GridBookmarkWidget', 'GridBookmark', {
+                        view: self
+                      });
+                    }
+
+                    session.showWidget(bookmarkWidget);
+                    return bookmarkWidget;
+                  }
+
+                  throw new Error('Could not open bookmark widget');
+                },
+                bookmarkCurrentRegion: function bookmarkCurrentRegion() {
+                  var selectedRegions = self.getSelectedRegions(self.leftOffset, self.rightOffset);
+                  var firstRegion = selectedRegions[0];
+                  var session = (0, _util.getSession)(self);
+
+                  if ((0, _util.isSessionModelWithWidgets)(session)) {
+                    var widgets = session.widgets;
+                    var bookmarkWidget = widgets.get('GridBookmark');
+
+                    if (!bookmarkWidget) {
+                      this.activateBookmarkWidget();
+                      bookmarkWidget = widgets.get('GridBookmark');
+                    } // @ts-ignore
+
+
+                    bookmarkWidget.addBookmark(firstRegion);
+                  }
+                }
+              },
+              views: {
+                menuItems: function menuItems() {
+                  var newMenuItems = [].concat((0, _toConsumableArray2["default"])(superMenuItems()), [{
+                    type: 'divider'
+                  }, {
+                    label: 'Open bookmark widget',
+                    icon: _Bookmarks["default"],
+                    // @ts-ignore
+                    onClick: self.activateBookmarkWidget
+                  }, {
+                    label: 'Bookmark current region',
+                    icon: _Bookmark["default"],
+                    // @ts-ignore
+                    onClick: self.bookmarkCurrentRegion
+                  }]);
+                  return newMenuItems;
+                },
+                rubberBandMenuItems: function rubberBandMenuItems() {
+                  var newRubberBandMenuItems = [].concat((0, _toConsumableArray2["default"])(superRubberBandMenuItems()), [{
+                    label: 'Bookmark region',
+                    icon: _Bookmark["default"],
+                    onClick: function onClick() {
+                      var leftOffset = self.leftOffset,
+                          rightOffset = self.rightOffset;
+                      var selectedRegions = self.getSelectedRegions(leftOffset, rightOffset);
+                      var firstRegion = selectedRegions[0];
+                      var session = (0, _util.getSession)(self);
+
+                      if ((0, _util.isSessionModelWithWidgets)(session)) {
+                        var widgets = session.widgets;
+                        var bookmarkWidget = widgets.get('GridBookmark');
+
+                        if (!bookmarkWidget) {
+                          // @ts-ignore
+                          self.activateBookmarkWidget();
+                          bookmarkWidget = widgets.get('GridBookmark');
+                        } // @ts-ignore
+
+
+                        bookmarkWidget.addBookmark(firstRegion);
+                      }
+                    }
+                  }]);
+                  return newRubberBandMenuItems;
+                }
+              }
+            };
+          });
+          pluggableElement.stateModel = newStateModel;
+        }
+
+        return pluggableElement;
+      });
+    }
+  }, {
+    key: "configure",
+    value: function configure(_pluginManager) {}
+  }]);
+  return _default;
+}(_Plugin2["default"]);
+
+exports["default"] = _default;

package/dist/index.test.js

@@ -0,0 +1,35 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+var _PluginManager = _interopRequireDefault(require("@jbrowse/core/PluginManager"));
+
+var _pluginConfig = _interopRequireDefault(require("@jbrowse/plugin-config"));
+
+var _mobxStateTree = require("mobx-state-tree");
+
+var _ = _interopRequireDefault(require("."));
+
+describe('Grid bookmark', function () {
+  var pluginManager;
+  beforeAll(function () {
+    var originalConsoleWarn = console.warn;
+    console.warn = jest.fn();
+    pluginManager = new _PluginManager["default"]([new _["default"](), new _pluginConfig["default"]()]);
+    pluginManager.createPluggableElements();
+    pluginManager.configure();
+    console.warn = originalConsoleWarn;
+  });
+  it("won't add if already added", function () {
+    expect(function () {
+      return pluginManager.addPlugin(new _["default"]());
+    }).toThrow(/JBrowse already configured, cannot add plugins/);
+  });
+  it('adds grid bookmark widget', function () {
+    var GridBookmarkWidget = pluginManager.getWidgetType('GridBookmarkWidget');
+    var config = GridBookmarkWidget.configSchema.create({
+      type: 'GridBookmarkWidget'
+    });
+    expect((0, _mobxStateTree.getSnapshot)(config)).toMatchSnapshot();
+  });
+});

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-grid-bookmark",
-  "version": "1.6.9",
+  "version": "1.7.3",
   "description": "JBrowse 2 grid bookmark widget",
   "keywords": [
     "jbrowse",
@@ -18,21 +18,19 @@
   "distMain": "dist/index.js",
   "srcMain": "src/index.ts",
   "main": "dist/index.js",
-  "distModule": "dist/plugin-grid-bookmark.esm.js",
-  "module": "dist/plugin-grid-bookmark.esm.js",
   "files": [
     "dist",
     "src"
   ],
   "scripts": {
-    "start": "tsdx watch --verbose --noClean",
-    "build": "tsdx build",
+    "build": "babel src --root-mode upward --out-dir dist --extensions .ts,.js,.tsx,.jsx",
     "test": "cd ../..; jest plugins/grid-bookmark",
     "prepublishOnly": "yarn test",
     "prepack": "yarn build; yarn useDist",
     "postpack": "yarn useSrc",
     "useDist": "node ../../scripts/useDist.js",
-    "useSrc": "node ../../scripts/useSrc.js"
+    "useSrc": "node ../../scripts/useSrc.js",
+    "postbuild": "tsc --build tsconfig.build.json"
   },
   "dependencies": {
     "@material-ui/icons": "^4.9.1",
@@ -53,5 +51,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "f6c3d4edfadc26f7ac635a2fa7259f50f0c7e5e3"
+  "gitHead": "09b13c85acf4ac68dd71ab23af87656c7552fdaf"
 }

package/src/GridBookmarkWidget/components/GridBookmarkWidget.test.js

@@ -5,6 +5,7 @@ import { render, cleanup, fireEvent, within } from '@testing-library/react'
 import { createTestSession } from '@jbrowse/web/src/rootModel'
 
 import GridBookmarkWidget from './GridBookmarkWidget'
+jest.mock('@jbrowse/web/src/makeWorkerInstance', () => () => {})
 
 jest.mock('file-saver', () => {
   return {

package/src/GridBookmarkWidget/types.ts

@@ -1,5 +1,4 @@
-import { AbstractViewModel } from '@jbrowse/core/util/types'
-import { Region } from '@jbrowse/core/util/types'
+import { AbstractViewModel, Region } from '@jbrowse/core/util/types'
 
 export interface NavigableViewModel extends AbstractViewModel {
   navToLocString: Function

package/src/index.ts

@@ -7,9 +7,8 @@ import WidgetType from '@jbrowse/core/pluggableElementTypes/WidgetType'
 import Plugin from '@jbrowse/core/Plugin'
 import PluginManager from '@jbrowse/core/PluginManager'
 import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
-import { getSession } from '@jbrowse/core/util'
+import { getSession, isSessionModelWithWidgets } from '@jbrowse/core/util'
 import ViewType from '@jbrowse/core/pluggableElementTypes/ViewType'
-import { isSessionModelWithWidgets } from '@jbrowse/core/util'
 
 import {
   stateModelFactory as GridBookmarkStateModelFactory,

package/dist/GridBookmarkWidget/components/GridBookmarkWidget.test.d.ts

@@ -1 +0,0 @@
-export {};

package/dist/index.test.d.ts

@@ -1 +0,0 @@
-export {};