@jbrowse/plugin-data-management 1.6.7 → 1.7.0

package/dist/AssemblyManager/AssemblyManager.test.js

@@ -0,0 +1,113 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+var _react = _interopRequireDefault(require("react"));
+
+var _react2 = require("@testing-library/react");
+
+var _AssemblyManager = _interopRequireDefault(require("./AssemblyManager"));
+
+var mockRootModel = {
+  jbrowse: {
+    assemblies: [{
+      name: 'testAssembly',
+      sequence: {
+        type: 'testSequenceTrack',
+        trackId: '',
+        adapter: {
+          type: 'testSeqAdapter',
+          twoBitLocation: {
+            uri: 'test.2bit',
+            locationType: 'UriLocation'
+          }
+        }
+      }
+    }],
+    addAssemblyConf: jest.fn(),
+    removeAssemblyConf: jest.fn()
+  },
+  session: {
+    notify: jest.fn()
+  }
+};
+describe('AssemblyManager GUI', function () {
+  it('renders succesfully', function () {
+    var _render = (0, _react2.render)( /*#__PURE__*/_react["default"].createElement(_AssemblyManager["default"], {
+      rootModel: mockRootModel,
+      onClose: function onClose() {}
+    })),
+        getByText = _render.getByText;
+
+    expect(getByText('Assembly manager')).toBeTruthy();
+  });
+  it('opens up the Add Assembly Form when clicked', function () {
+    var _render2 = (0, _react2.render)( /*#__PURE__*/_react["default"].createElement(_AssemblyManager["default"], {
+      rootModel: mockRootModel,
+      onClose: function onClose() {}
+    })),
+        getByText = _render2.getByText;
+
+    _react2.fireEvent.click(getByText('Add new assembly'));
+
+    expect(getByText('Create new assembly')).toBeTruthy();
+  });
+  it('calls addAssemblyConf from the Add Assembly form', function () {
+    var _render3 = (0, _react2.render)( /*#__PURE__*/_react["default"].createElement(_AssemblyManager["default"], {
+      rootModel: mockRootModel,
+      onClose: function onClose() {}
+    })),
+        getByText = _render3.getByText,
+        getByTestId = _render3.getByTestId;
+
+    _react2.fireEvent.click(getByText('Add new assembly')); // enter a new assembly and submit
+
+
+    _react2.fireEvent.change(getByTestId('assembly-name'), {
+      target: {
+        value: 'ce11'
+      }
+    });
+
+    _react2.fireEvent.click(getByText('Create new assembly'));
+
+    expect(mockRootModel.jbrowse.addAssemblyConf).toHaveBeenCalledTimes(1);
+  });
+  it("prompts the user for a name when adding assembly if they don't", function () {
+    var _render4 = (0, _react2.render)( /*#__PURE__*/_react["default"].createElement(_AssemblyManager["default"], {
+      rootModel: mockRootModel,
+      onClose: function onClose() {}
+    })),
+        getByText = _render4.getByText;
+
+    _react2.fireEvent.click(getByText('Add new assembly'));
+
+    _react2.fireEvent.click(getByText('Create new assembly'));
+
+    expect(mockRootModel.session.notify).toHaveBeenCalledWith("Can't create an assembly without a name");
+  });
+  it('deletes an assembly when delete button clicked', function () {
+    var _render5 = (0, _react2.render)( /*#__PURE__*/_react["default"].createElement(_AssemblyManager["default"], {
+      rootModel: mockRootModel,
+      onClose: function onClose() {}
+    })),
+        getByTestId = _render5.getByTestId;
+
+    _react2.fireEvent.click(getByTestId('testAssembly-delete'));
+
+    expect(mockRootModel.jbrowse.removeAssemblyConf).toHaveBeenCalledWith('testAssembly');
+  });
+  it('closes when the Close button is clicked', function () {
+    var onClose = jest.fn();
+
+    var _render6 = (0, _react2.render)( /*#__PURE__*/_react["default"].createElement(_AssemblyManager["default"], {
+      rootModel: mockRootModel,
+      onClose: onClose
+    })),
+        getByText = _render6.getByText;
+
+    _react2.fireEvent.click(getByText('Close'));
+
+    expect(onClose).toHaveBeenCalled();
+  });
+});

package/dist/AssemblyManager/AssemblyTable.js

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+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _react = _interopRequireDefault(require("react"));
+
+var _mobxReact = require("mobx-react");
+
+var _core = require("@material-ui/core");
+
+var _Create = _interopRequireDefault(require("@material-ui/icons/Create"));
+
+var _Delete = _interopRequireDefault(require("@material-ui/icons/Delete"));
+
+var _configuration = require("@jbrowse/core/configuration");
+
+// local
+var useStyles = (0, _core.makeStyles)(function () {
+  return {
+    table: {
+      minWidth: 500,
+      minHeight: 150
+    },
+    buttonCell: {
+      padding: 3
+    },
+    button: {
+      display: 'inline-block',
+      padding: 3,
+      minHeight: 0,
+      minWidth: 0
+    }
+  };
+});
+var AssemblyTable = (0, _mobxReact.observer)(function (_ref) {
+  var rootModel = _ref.rootModel,
+      setIsAssemblyBeingEdited = _ref.setIsAssemblyBeingEdited,
+      setAssemblyBeingEdited = _ref.setAssemblyBeingEdited;
+  var classes = useStyles();
+
+  function removeAssembly(name) {
+    rootModel.jbrowse.removeAssemblyConf(name);
+  }
+
+  var rows = rootModel.jbrowse.assemblies.map(function (assembly) {
+    var name = (0, _configuration.readConfObject)(assembly, 'name');
+    var displayName = (0, _configuration.readConfObject)(assembly, 'displayName');
+    var aliases = (0, _configuration.readConfObject)(assembly, 'aliases');
+    return /*#__PURE__*/_react["default"].createElement(_core.TableRow, {
+      key: name
+    }, /*#__PURE__*/_react["default"].createElement(_core.TableCell, null, name), /*#__PURE__*/_react["default"].createElement(_core.TableCell, null, displayName), /*#__PURE__*/_react["default"].createElement(_core.TableCell, null, aliases ? aliases.toString() : ''), /*#__PURE__*/_react["default"].createElement(_core.TableCell, {
+      className: classes.buttonCell
+    }, /*#__PURE__*/_react["default"].createElement(_core.IconButton, {
+      "data-testid": "".concat(name, "-edit"),
+      className: classes.button,
+      onClick: function onClick() {
+        setIsAssemblyBeingEdited(true);
+        setAssemblyBeingEdited(assembly);
+      }
+    }, /*#__PURE__*/_react["default"].createElement(_Create["default"], {
+      color: "primary"
+    })), /*#__PURE__*/_react["default"].createElement(_core.IconButton, {
+      "data-testid": "".concat(name, "-delete"),
+      className: classes.button,
+      onClick: function onClick() {
+        removeAssembly(name);
+      }
+    }, /*#__PURE__*/_react["default"].createElement(_Delete["default"], {
+      color: "error"
+    }))));
+  });
+  return /*#__PURE__*/_react["default"].createElement(_core.TableContainer, {
+    component: _core.Paper
+  }, /*#__PURE__*/_react["default"].createElement(_core.Table, {
+    className: classes.table
+  }, /*#__PURE__*/_react["default"].createElement(_core.TableHead, null, /*#__PURE__*/_react["default"].createElement(_core.TableRow, null, /*#__PURE__*/_react["default"].createElement(_core.TableCell, null, /*#__PURE__*/_react["default"].createElement(_core.Typography, {
+    variant: "h5"
+  }, "Name")), /*#__PURE__*/_react["default"].createElement(_core.TableCell, null, /*#__PURE__*/_react["default"].createElement(_core.Typography, {
+    variant: "h5"
+  }, "Display name")), /*#__PURE__*/_react["default"].createElement(_core.TableCell, null, /*#__PURE__*/_react["default"].createElement(_core.Typography, {
+    variant: "h5"
+  }, "Aliases")), /*#__PURE__*/_react["default"].createElement(_core.TableCell, null, /*#__PURE__*/_react["default"].createElement(_core.Typography, {
+    variant: "h5"
+  }, "Actions")))), /*#__PURE__*/_react["default"].createElement(_core.TableBody, null, rows)));
+});
+var _default = AssemblyTable;
+exports["default"] = _default;

package/dist/AssemblyManager/index.js

@@ -0,0 +1,15 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+Object.defineProperty(exports, "default", {
+  enumerable: true,
+  get: function get() {
+    return _AssemblyManager["default"];
+  }
+});
+
+var _AssemblyManager = _interopRequireDefault(require("./AssemblyManager"));

package/dist/HierarchicalTrackSelectorWidget/components/CloseConnectionDialog.js

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+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
+
+var _react = _interopRequireDefault(require("react"));
+
+var _core = require("@material-ui/core");
+
+var _mobxReact = require("mobx-react");
+
+function CloseConnectionDialog(_ref) {
+  var _ref$modalInfo = _ref.modalInfo,
+      modalInfo = _ref$modalInfo === void 0 ? {} : _ref$modalInfo,
+      setModalInfo = _ref.setModalInfo;
+  var name = modalInfo.name,
+      dereferenceTypeCount = modalInfo.dereferenceTypeCount,
+      safelyBreakConnection = modalInfo.safelyBreakConnection;
+  return /*#__PURE__*/_react["default"].createElement(_core.Dialog, {
+    open: true
+  }, /*#__PURE__*/_react["default"].createElement(_core.DialogTitle, null, "Close connection \"", name, "\""), /*#__PURE__*/_react["default"].createElement(_core.DialogContent, null, dereferenceTypeCount ? /*#__PURE__*/_react["default"].createElement(_react["default"].Fragment, null, /*#__PURE__*/_react["default"].createElement(_core.DialogContentText, null, "Closing this connection will close:"), /*#__PURE__*/_react["default"].createElement(_core.List, null, Object.entries(dereferenceTypeCount).map(function (_ref2) {
+    var _ref3 = (0, _slicedToArray2["default"])(_ref2, 2),
+        key = _ref3[0],
+        value = _ref3[1];
+
+    return /*#__PURE__*/_react["default"].createElement(_core.ListItem, {
+      key: key
+    }, "".concat(value, " ").concat(key));
+  }))) : null, /*#__PURE__*/_react["default"].createElement(_core.DialogContentText, null, "Are you sure you want to close this connection?")), /*#__PURE__*/_react["default"].createElement(_core.DialogActions, null, /*#__PURE__*/_react["default"].createElement(_core.Button, {
+    onClick: function onClick() {
+      setModalInfo();
+    },
+    color: "primary"
+  }, "Cancel"), /*#__PURE__*/_react["default"].createElement(_core.Button, {
+    variant: "contained",
+    onClick: modalInfo ? function () {
+      if (safelyBreakConnection) {
+        safelyBreakConnection();
+      }
+
+      setModalInfo();
+    } : function () {},
+    color: "primary"
+  }, "OK")));
+}
+
+var _default = (0, _mobxReact.observer)(CloseConnectionDialog);
+
+exports["default"] = _default;

package/dist/HierarchicalTrackSelectorWidget/components/DeleteConnectionDialog.js

@@ -0,0 +1,46 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _react = _interopRequireDefault(require("react"));
+
+var _core = require("@material-ui/core");
+
+var _mobxReact = require("mobx-react");
+
+function DeleteConnectionDialog(_ref) {
+  var deleteDialogDetails = _ref.deleteDialogDetails,
+      session = _ref.session,
+      handleClose = _ref.handleClose;
+  var connectionConf = deleteDialogDetails.connectionConf,
+      name = deleteDialogDetails.name;
+  return /*#__PURE__*/_react["default"].createElement(_core.Dialog, {
+    open: true
+  }, /*#__PURE__*/_react["default"].createElement(_core.DialogTitle, null, "Delete connection \"", name, "\""), /*#__PURE__*/_react["default"].createElement(_core.DialogContent, null, /*#__PURE__*/_react["default"].createElement(_core.DialogContentText, null, "Are you sure you want to delete this connection?")), /*#__PURE__*/_react["default"].createElement(_core.DialogActions, null, /*#__PURE__*/_react["default"].createElement(_core.Button, {
+    onClick: function onClick() {
+      return handleClose();
+    },
+    color: "primary"
+  }, "Cancel"), /*#__PURE__*/_react["default"].createElement(_core.Button, {
+    variant: "contained",
+    color: "primary",
+    onClick: function onClick() {
+      if (connectionConf) {
+        var _session$deleteConnec;
+
+        (_session$deleteConnec = session.deleteConnection) === null || _session$deleteConnec === void 0 ? void 0 : _session$deleteConnec.call(session, connectionConf);
+      }
+
+      handleClose();
+    }
+  }, "OK")));
+}
+
+var _default = (0, _mobxReact.observer)(DeleteConnectionDialog);
+
+exports["default"] = _default;