@jbrowse/plugin-grid-bookmark 1.6.7 → 1.7.0

package/dist/GridBookmarkWidget/components/GridBookmarkWidget.test.js

@@ -0,0 +1,302 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+
+var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
+
+var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
+
+var _react = _interopRequireDefault(require("react"));
+
+var _fileSaver = require("file-saver");
+
+var _react2 = require("@testing-library/react");
+
+var _rootModel = require("@jbrowse/web/src/rootModel");
+
+var _GridBookmarkWidget = _interopRequireDefault(require("./GridBookmarkWidget"));
+
+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; }
+
+jest.mock('@jbrowse/web/src/makeWorkerInstance', function () {
+  return function () {};
+});
+jest.mock('file-saver', function () {
+  return _objectSpread(_objectSpread({}, jest.requireActual('file-saver')), {}, {
+    saveAs: jest.fn()
+  });
+});
+describe('<GridBookmarkWidget />', function () {
+  var session;
+  var model;
+  beforeEach(function () {
+    session = (0, _rootModel.createTestSession)();
+    model = session.addWidget('GridBookmarkWidget', 'gridBookmarkWidget');
+
+    _fileSaver.saveAs.mockReset();
+  });
+  afterEach(_react2.cleanup);
+  it('renders empty with no bookmarks', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+    var _render, findByText;
+
+    return _regenerator["default"].wrap(function _callee$(_context) {
+      while (1) {
+        switch (_context.prev = _context.next) {
+          case 0:
+            _render = (0, _react2.render)( /*#__PURE__*/_react["default"].createElement(_GridBookmarkWidget["default"], {
+              model: model
+            })), findByText = _render.findByText;
+            _context.t0 = expect;
+            _context.next = 4;
+            return findByText('No rows');
+
+          case 4:
+            _context.t1 = _context.sent;
+            (0, _context.t0)(_context.t1).toBeTruthy();
+
+          case 6:
+          case "end":
+            return _context.stop();
+        }
+      }
+    }, _callee);
+  })));
+  it('renders bookmarks correctly', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2() {
+    var _render2, findByText;
+
+    return _regenerator["default"].wrap(function _callee2$(_context2) {
+      while (1) {
+        switch (_context2.prev = _context2.next) {
+          case 0:
+            model.addBookmark({
+              refName: 'chr1',
+              start: 1,
+              end: 12,
+              assemblyName: 'hg19'
+            });
+            _render2 = (0, _react2.render)( /*#__PURE__*/_react["default"].createElement(_GridBookmarkWidget["default"], {
+              model: model
+            })), findByText = _render2.findByText;
+            _context2.t0 = expect;
+            _context2.next = 5;
+            return findByText('chr1:2..12');
+
+          case 5:
+            _context2.t1 = _context2.sent;
+            (0, _context2.t0)(_context2.t1).toBeTruthy();
+
+          case 7:
+          case "end":
+            return _context2.stop();
+        }
+      }
+    }, _callee2);
+  })));
+  it('deletes individual bookmarks correctly', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee3() {
+    var _render3, findByText, findByTestId;
+
+    return _regenerator["default"].wrap(function _callee3$(_context3) {
+      while (1) {
+        switch (_context3.prev = _context3.next) {
+          case 0:
+            model.addBookmark({
+              refName: 'chr1',
+              start: 1,
+              end: 12,
+              assemblyName: 'hg19'
+            });
+            _render3 = (0, _react2.render)( /*#__PURE__*/_react["default"].createElement(_GridBookmarkWidget["default"], {
+              model: model
+            })), findByText = _render3.findByText, findByTestId = _render3.findByTestId;
+            _context3.t0 = _react2.fireEvent;
+            _context3.next = 5;
+            return findByTestId('deleteBookmark');
+
+          case 5:
+            _context3.t1 = _context3.sent;
+
+            _context3.t0.click.call(_context3.t0, _context3.t1);
+
+            _context3.t2 = _react2.fireEvent;
+            _context3.next = 10;
+            return findByText('Confirm');
+
+          case 10:
+            _context3.t3 = _context3.sent;
+
+            _context3.t2.click.call(_context3.t2, _context3.t3);
+
+            _context3.t4 = expect;
+            _context3.next = 15;
+            return findByText('No rows');
+
+          case 15:
+            _context3.t5 = _context3.sent;
+            (0, _context3.t4)(_context3.t5).toBeTruthy();
+
+          case 17:
+          case "end":
+            return _context3.stop();
+        }
+      }
+    }, _callee3);
+  })));
+  it('clears all bookmarks correctly', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee4() {
+    var _render4, findByText;
+
+    return _regenerator["default"].wrap(function _callee4$(_context4) {
+      while (1) {
+        switch (_context4.prev = _context4.next) {
+          case 0:
+            model.addBookmark({
+              refName: 'chr1',
+              start: 1,
+              end: 12,
+              assemblyName: 'hg19'
+            });
+            _render4 = (0, _react2.render)( /*#__PURE__*/_react["default"].createElement(_GridBookmarkWidget["default"], {
+              model: model
+            })), findByText = _render4.findByText;
+            _context4.t0 = _react2.fireEvent;
+            _context4.next = 5;
+            return findByText('Clear');
+
+          case 5:
+            _context4.t1 = _context4.sent;
+
+            _context4.t0.click.call(_context4.t0, _context4.t1);
+
+            _context4.t2 = _react2.fireEvent;
+            _context4.next = 10;
+            return findByText('Confirm');
+
+          case 10:
+            _context4.t3 = _context4.sent;
+
+            _context4.t2.click.call(_context4.t2, _context4.t3);
+
+            _context4.t4 = expect;
+            _context4.next = 15;
+            return findByText('No rows');
+
+          case 15:
+            _context4.t5 = _context4.sent;
+            (0, _context4.t4)(_context4.t5).toBeTruthy();
+
+          case 17:
+          case "end":
+            return _context4.stop();
+        }
+      }
+    }, _callee4);
+  })));
+  it('downloads a BED file correctly', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee5() {
+    var _render5, findByText, findByTestId, blob;
+
+    return _regenerator["default"].wrap(function _callee5$(_context5) {
+      while (1) {
+        switch (_context5.prev = _context5.next) {
+          case 0:
+            model.addBookmark({
+              refName: 'chr1',
+              start: 1,
+              end: 12,
+              assemblyName: 'hg19'
+            });
+            _render5 = (0, _react2.render)( /*#__PURE__*/_react["default"].createElement(_GridBookmarkWidget["default"], {
+              model: model
+            })), findByText = _render5.findByText, findByTestId = _render5.findByTestId;
+            _context5.t0 = _react2.fireEvent;
+            _context5.next = 5;
+            return findByText('Download');
+
+          case 5:
+            _context5.t1 = _context5.sent;
+
+            _context5.t0.click.call(_context5.t0, _context5.t1);
+
+            _context5.t2 = _react2.fireEvent;
+            _context5.next = 10;
+            return findByTestId('dialogDownload');
+
+          case 10:
+            _context5.t3 = _context5.sent;
+
+            _context5.t2.click.call(_context5.t2, _context5.t3);
+
+            blob = new Blob([''], {
+              type: 'text/x-bed;charset=utf-8'
+            });
+            expect(_fileSaver.saveAs).toHaveBeenCalledWith(blob, 'jbrowse_bookmarks_hg19.bed');
+
+          case 14:
+          case "end":
+            return _context5.stop();
+        }
+      }
+    }, _callee5);
+  })));
+  it('downloads a TSV file correctly', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee6() {
+    var _render6, findByText, findByTestId, getByRole, listbox, blob;
+
+    return _regenerator["default"].wrap(function _callee6$(_context6) {
+      while (1) {
+        switch (_context6.prev = _context6.next) {
+          case 0:
+            model.addBookmark({
+              refName: 'chr1',
+              start: 1,
+              end: 12,
+              assemblyName: 'hg19'
+            });
+            _render6 = (0, _react2.render)( /*#__PURE__*/_react["default"].createElement(_GridBookmarkWidget["default"], {
+              model: model
+            })), findByText = _render6.findByText, findByTestId = _render6.findByTestId, getByRole = _render6.getByRole;
+            _context6.t0 = _react2.fireEvent;
+            _context6.next = 5;
+            return findByText('Download');
+
+          case 5:
+            _context6.t1 = _context6.sent;
+
+            _context6.t0.click.call(_context6.t0, _context6.t1);
+
+            _context6.t2 = _react2.fireEvent;
+            _context6.next = 10;
+            return findByText('BED');
+
+          case 10:
+            _context6.t3 = _context6.sent;
+
+            _context6.t2.mouseDown.call(_context6.t2, _context6.t3);
+
+            listbox = (0, _react2.within)(getByRole('listbox'));
+
+            _react2.fireEvent.click(listbox.getByText('TSV'));
+
+            _context6.t4 = _react2.fireEvent;
+            _context6.next = 17;
+            return findByTestId('dialogDownload');
+
+          case 17:
+            _context6.t5 = _context6.sent;
+
+            _context6.t4.click.call(_context6.t4, _context6.t5);
+
+            blob = new Blob([''], {
+              type: 'text/tab-separated-values;charset=utf-8'
+            });
+            expect(_fileSaver.saveAs).toHaveBeenCalledWith(blob, 'jbrowse_bookmarks.tsv');
+
+          case 21:
+          case "end":
+            return _context6.stop();
+        }
+      }
+    }, _callee6);
+  })));
+});

package/dist/GridBookmarkWidget/components/ImportBookmarks.js

@@ -0,0 +1,190 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+var _typeof = require("@babel/runtime/helpers/typeof");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+
+var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
+
+var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
+
+var _react = _interopRequireWildcard(require("react"));
+
+var _mobxReact = require("mobx-react");
+
+var _util = require("@jbrowse/core/util");
+
+var _AssemblySelector = _interopRequireDefault(require("@jbrowse/core/ui/AssemblySelector"));
+
+var _ui = require("@jbrowse/core/ui");
+
+var _io = require("@jbrowse/core/util/io");
+
+var _core = require("@material-ui/core");
+
+var _Close = _interopRequireDefault(require("@material-ui/icons/Close"));
+
+var _Publish = _interopRequireDefault(require("@material-ui/icons/Publish"));
+
+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; }
+
+var useStyles = (0, _core.makeStyles)(function () {
+  return {
+    closeDialog: {
+      position: 'absolute',
+      right: 0,
+      top: 0
+    },
+    dialogContainer: {
+      margin: 15
+    },
+    flexItem: {
+      margin: 5
+    }
+  };
+});
+
+function ImportBookmarks(_ref) {
+  var model = _ref.model,
+      assemblyName = _ref.assemblyName;
+  var classes = useStyles();
+  var session = (0, _util.getSession)(model);
+  var assemblyNames = session.assemblyNames;
+
+  var _useState = (0, _react.useState)(false),
+      _useState2 = (0, _slicedToArray2["default"])(_useState, 2),
+      dialogOpen = _useState2[0],
+      setDialogOpen = _useState2[1];
+
+  var _useState3 = (0, _react.useState)(),
+      _useState4 = (0, _slicedToArray2["default"])(_useState3, 2),
+      location = _useState4[0],
+      setLocation = _useState4[1];
+
+  var _useState5 = (0, _react.useState)(),
+      _useState6 = (0, _slicedToArray2["default"])(_useState5, 2),
+      error = _useState6[0],
+      setError = _useState6[1];
+
+  var _useState7 = (0, _react.useState)(assemblyName || assemblyNames[0]),
+      _useState8 = (0, _slicedToArray2["default"])(_useState7, 2),
+      selectedAsm = _useState8[0],
+      setSelectedAsm = _useState8[1];
+
+  return /*#__PURE__*/_react["default"].createElement(_react["default"].Fragment, null, /*#__PURE__*/_react["default"].createElement(_core.Button, {
+    startIcon: /*#__PURE__*/_react["default"].createElement(_Publish["default"], null),
+    onClick: function onClick() {
+      return setDialogOpen(true);
+    }
+  }, "Import"), /*#__PURE__*/_react["default"].createElement(_core.Dialog, {
+    open: dialogOpen,
+    onClose: function onClose() {
+      return setDialogOpen(false);
+    },
+    maxWidth: "xl"
+  }, /*#__PURE__*/_react["default"].createElement(_core.DialogTitle, null, "Import bookmarks", /*#__PURE__*/_react["default"].createElement(_core.IconButton, {
+    className: classes.closeDialog,
+    "aria-label": "close-dialog",
+    onClick: function onClick() {
+      return setDialogOpen(false);
+    }
+  }, /*#__PURE__*/_react["default"].createElement(_Close["default"], null))), /*#__PURE__*/_react["default"].createElement(_core.DialogContent, null, /*#__PURE__*/_react["default"].createElement(_core.Typography, null, "Choose a BED format file to import. The first 4 columns will be used"), /*#__PURE__*/_react["default"].createElement(_ui.FileSelector, {
+    location: location,
+    setLocation: setLocation,
+    name: "File"
+  }), /*#__PURE__*/_react["default"].createElement(_core.Typography, null, "Select assembly that your data belongs to"), /*#__PURE__*/_react["default"].createElement(_AssemblySelector["default"], {
+    onChange: function onChange(val) {
+      return setSelectedAsm(val);
+    },
+    session: session,
+    selected: selectedAsm
+  }), error ? /*#__PURE__*/_react["default"].createElement(_core.Typography, {
+    color: "error",
+    variant: "h6"
+  }, "".concat(error)) : null), /*#__PURE__*/_react["default"].createElement(_core.DialogActions, null, /*#__PURE__*/_react["default"].createElement(_core.Button, {
+    variant: "contained",
+    color: "secondary",
+    onClick: function onClick() {
+      return setDialogOpen(false);
+    }
+  }, "Cancel"), /*#__PURE__*/_react["default"].createElement(_core.Button, {
+    className: classes.flexItem,
+    "data-testid": "dialogImport",
+    variant: "contained",
+    color: "primary",
+    disabled: !location,
+    startIcon: /*#__PURE__*/_react["default"].createElement(_Publish["default"], null),
+    onClick: /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+      var data, regions;
+      return _regenerator["default"].wrap(function _callee$(_context) {
+        while (1) {
+          switch (_context.prev = _context.next) {
+            case 0:
+              _context.prev = 0;
+
+              if (location) {
+                _context.next = 3;
+                break;
+              }
+
+              return _context.abrupt("return");
+
+            case 3:
+              _context.next = 5;
+              return (0, _io.openLocation)(location).readFile('utf8');
+
+            case 5:
+              data = _context.sent;
+              regions = data.split('\n').filter(function (f) {
+                return !!f.trim();
+              }).filter(function (f) {
+                return !f.startsWith('#') && !f.startsWith('track') && !f.startsWith('browser');
+              }).map(function (line) {
+                var _line$split = line.split('\t'),
+                    _line$split2 = (0, _slicedToArray2["default"])(_line$split, 4),
+                    refName = _line$split2[0],
+                    start = _line$split2[1],
+                    end = _line$split2[2],
+                    name = _line$split2[3];
+
+                return {
+                  assemblyName: selectedAsm,
+                  refName: refName,
+                  start: +start,
+                  end: +end,
+                  label: name === '.' ? undefined : name
+                };
+              });
+              model.importBookmarks(regions);
+              setDialogOpen(false);
+              _context.next = 15;
+              break;
+
+            case 11:
+              _context.prev = 11;
+              _context.t0 = _context["catch"](0);
+              console.error(_context.t0);
+              setError(_context.t0);
+
+            case 15:
+            case "end":
+              return _context.stop();
+          }
+        }
+      }, _callee, null, [[0, 11]]);
+    }))
+  }, "Import"))));
+}
+
+var _default = (0, _mobxReact.observer)(ImportBookmarks);
+
+exports["default"] = _default;

package/dist/GridBookmarkWidget/index.js

@@ -0,0 +1,29 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+Object.defineProperty(exports, "ReactComponent", {
+  enumerable: true,
+  get: function get() {
+    return _GridBookmarkWidget["default"];
+  }
+});
+exports.configSchema = void 0;
+Object.defineProperty(exports, "stateModelFactory", {
+  enumerable: true,
+  get: function get() {
+    return _model["default"];
+  }
+});
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _GridBookmarkWidget = _interopRequireDefault(require("./components/GridBookmarkWidget"));
+
+var _model = _interopRequireDefault(require("./model"));
+
+var configSchema = (0, _configuration.ConfigurationSchema)('GridBookmarkWidget', {});
+exports.configSchema = configSchema;

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.js

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