@jbrowse/plugin-data-management 1.6.9 → 1.7.0

package/dist/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.test.js

@@ -0,0 +1,191 @@
+"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 _rootModel = require("@jbrowse/web/src/rootModel");
+
+var _styles = require("@material-ui/core/styles");
+
+var _react = require("@testing-library/react");
+
+var _react2 = _interopRequireDefault(require("react"));
+
+var _HierarchicalTrackSelector = _interopRequireDefault(require("./HierarchicalTrackSelector"));
+
+jest.mock('@jbrowse/web/src/makeWorkerInstance', function () {
+  return function () {};
+});
+
+window.requestIdleCallback = function (cb) {
+  return cb();
+};
+
+window.cancelIdleCallback = function () {};
+
+describe('HierarchicalTrackSelector widget', function () {
+  afterEach(_react.cleanup);
+  it('renders nothing with no assembly', function () {
+    var session = (0, _rootModel.createTestSession)();
+    var firstView = session.addView('LinearGenomeView');
+    var model = firstView.activateTrackSelector();
+
+    var _render = (0, _react.render)( /*#__PURE__*/_react2["default"].createElement(_styles.ThemeProvider, {
+      theme: (0, _styles.createTheme)()
+    }, /*#__PURE__*/_react2["default"].createElement(_HierarchicalTrackSelector["default"], {
+      model: model
+    }))),
+        container = _render.container;
+
+    expect(container.firstChild).toMatchSnapshot();
+  });
+  it('renders with a couple of uncategorized tracks', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+    var session, firstView, model, _render2, container, findByTestId;
+
+    return _regenerator["default"].wrap(function _callee$(_context) {
+      while (1) {
+        switch (_context.prev = _context.next) {
+          case 0:
+            session = (0, _rootModel.createTestSession)();
+            session.addAssemblyConf({
+              name: 'volMyt1',
+              sequence: {
+                trackId: 'sequenceConfigId',
+                type: 'ReferenceSequenceTrack',
+                adapter: {
+                  type: 'FromConfigSequenceAdapter',
+                  features: [{
+                    refName: 'ctgA',
+                    uniqueId: 'firstId',
+                    start: 0,
+                    end: 10,
+                    seq: 'cattgttgcg'
+                  }]
+                }
+              }
+            });
+            session.addTrackConf({
+              trackId: 'fooC',
+              assemblyNames: ['volMyt1'],
+              type: 'FeatureTrack',
+              adapter: {
+                type: 'FromConfigAdapter',
+                features: []
+              }
+            });
+            session.addTrackConf({
+              trackId: 'barC',
+              assemblyNames: ['volMyt1'],
+              type: 'FeatureTrack',
+              adapter: {
+                type: 'FromConfigAdapter',
+                features: []
+              }
+            });
+            firstView = session.addView('LinearGenomeView', {
+              displayedRegions: [{
+                assemblyName: 'volMyt1',
+                refName: 'ctgA',
+                start: 0,
+                end: 1000
+              }]
+            });
+            firstView.showTrack(session.sessionTracks[0].trackId);
+            firstView.showTrack(session.sessionTracks[1].trackId);
+            model = firstView.activateTrackSelector();
+            _render2 = (0, _react.render)( /*#__PURE__*/_react2["default"].createElement(_styles.ThemeProvider, {
+              theme: (0, _styles.createTheme)()
+            }, /*#__PURE__*/_react2["default"].createElement(_HierarchicalTrackSelector["default"], {
+              model: model
+            }))), container = _render2.container, findByTestId = _render2.findByTestId;
+            _context.next = 11;
+            return findByTestId('hierarchical_track_selector');
+
+          case 11:
+            expect(container.firstChild).toMatchSnapshot();
+
+          case 12:
+          case "end":
+            return _context.stop();
+        }
+      }
+    }, _callee);
+  })));
+  it('renders with a couple of categorized tracks', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2() {
+    var session, firstView, model, _render3, container, findByTestId;
+
+    return _regenerator["default"].wrap(function _callee2$(_context2) {
+      while (1) {
+        switch (_context2.prev = _context2.next) {
+          case 0:
+            session = (0, _rootModel.createTestSession)();
+            session.addAssemblyConf({
+              name: 'volMyt1',
+              sequence: {
+                trackId: 'sequenceConfigId',
+                type: 'ReferenceSequenceTrack',
+                adapter: {
+                  type: 'FromConfigSequenceAdapter',
+                  features: [{
+                    refName: 'ctgA',
+                    uniqueId: 'firstId',
+                    start: 0,
+                    end: 10,
+                    seq: 'cattgttgcg'
+                  }]
+                }
+              }
+            });
+            session.addTrackConf({
+              trackId: 'fooC',
+              assemblyNames: ['volMyt1'],
+              type: 'FeatureTrack',
+              adapter: {
+                type: 'FromConfigAdapter',
+                features: []
+              }
+            });
+            session.addTrackConf({
+              trackId: 'barC',
+              assemblyNames: ['volMyt1'],
+              type: 'FeatureTrack',
+              adapter: {
+                type: 'FromConfigAdapter',
+                features: []
+              }
+            });
+            firstView = session.addView('LinearGenomeView', {
+              displayedRegions: [{
+                assemblyName: 'volMyt1',
+                refName: 'ctgA',
+                start: 0,
+                end: 1000
+              }]
+            });
+            firstView.showTrack(session.sessionTracks[0].trackId);
+            firstView.showTrack(session.sessionTracks[1].trackId);
+            firstView.tracks[0].configuration.category.set(['Foo Category']);
+            firstView.tracks[1].configuration.category.set(['Foo Category', 'Bar Category']);
+            model = firstView.activateTrackSelector();
+            _render3 = (0, _react.render)( /*#__PURE__*/_react2["default"].createElement(_styles.ThemeProvider, {
+              theme: (0, _styles.createTheme)()
+            }, /*#__PURE__*/_react2["default"].createElement(_HierarchicalTrackSelector["default"], {
+              model: model
+            }))), container = _render3.container, findByTestId = _render3.findByTestId;
+            _context2.next = 13;
+            return findByTestId('hierarchical_track_selector');
+
+          case 13:
+            expect(container.firstChild).toMatchSnapshot();
+
+          case 14:
+          case "end":
+            return _context2.stop();
+        }
+      }
+    }, _callee2);
+  })));
+});

package/dist/HierarchicalTrackSelectorWidget/components/ManageConnectionsDialog.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 _core = require("@material-ui/core");
+
+var _Close = _interopRequireDefault(require("@material-ui/icons/Close"));
+
+var _mobxReact = require("mobx-react");
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var useStyles = (0, _core.makeStyles)(function (theme) {
+  return {
+    closeButton: {
+      position: 'absolute',
+      right: theme.spacing(1),
+      top: theme.spacing(1),
+      color: theme.palette.grey[500]
+    },
+    connectionContainer: {
+      margin: theme.spacing(4),
+      width: 500
+    }
+  };
+});
+
+function ManageConnectionsDlg(_ref) {
+  var session = _ref.session,
+      handleClose = _ref.handleClose,
+      breakConnection = _ref.breakConnection;
+  var classes = useStyles();
+  var adminMode = session.adminMode,
+      connections = session.connections,
+      sessionConnections = session.sessionConnections;
+  return /*#__PURE__*/_react["default"].createElement(_core.Dialog, {
+    open: true,
+    onClose: handleClose,
+    maxWidth: "lg"
+  }, /*#__PURE__*/_react["default"].createElement(_core.DialogTitle, null, "Delete connections", /*#__PURE__*/_react["default"].createElement(_core.IconButton, {
+    className: classes.closeButton,
+    onClick: function onClick() {
+      return handleClose();
+    }
+  }, /*#__PURE__*/_react["default"].createElement(_Close["default"], null))), /*#__PURE__*/_react["default"].createElement(_core.DialogContent, null, /*#__PURE__*/_react["default"].createElement(_core.Typography, null, "Click the X icon to delete the connection from your config completely"), /*#__PURE__*/_react["default"].createElement("div", {
+    className: classes.connectionContainer
+  }, connections.map(function (conf) {
+    var name = (0, _configuration.readConfObject)(conf, 'name');
+    return /*#__PURE__*/_react["default"].createElement("div", {
+      key: "conn-".concat(name)
+    }, /*#__PURE__*/_react["default"].createElement(_core.Typography, null, adminMode || sessionConnections !== null && sessionConnections !== void 0 && sessionConnections.includes(conf) ? /*#__PURE__*/_react["default"].createElement(_core.IconButton, {
+      onClick: function onClick() {
+        return breakConnection(conf, true);
+      }
+    }, /*#__PURE__*/_react["default"].createElement(_Close["default"], {
+      color: "error"
+    })) : /*#__PURE__*/_react["default"].createElement(_core.Tooltip, {
+      title: "Unable to delete connection in config file as non-admin user"
+    }, /*#__PURE__*/_react["default"].createElement(_core.IconButton, null, /*#__PURE__*/_react["default"].createElement(_Close["default"], {
+      color: "disabled"
+    }))), name));
+  }), !connections.length ? /*#__PURE__*/_react["default"].createElement(_core.Typography, null, "No connections found") : null)), /*#__PURE__*/_react["default"].createElement(_core.DialogActions, null, /*#__PURE__*/_react["default"].createElement(_core.Button, {
+    onClick: function onClick() {
+      return handleClose();
+    },
+    variant: "contained",
+    color: "primary"
+  }, "Close")));
+}
+
+var _default = (0, _mobxReact.observer)(ManageConnectionsDlg);
+
+exports["default"] = _default;

package/dist/HierarchicalTrackSelectorWidget/components/ToggleConnectionsDialog.js

@@ -0,0 +1,98 @@
+"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 _Close = _interopRequireDefault(require("@material-ui/icons/Close"));
+
+var _mobxReact = require("mobx-react");
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var useStyles = (0, _core.makeStyles)(function (theme) {
+  return {
+    closeButton: {
+      position: 'absolute',
+      right: theme.spacing(1),
+      top: theme.spacing(1),
+      color: theme.palette.grey[500]
+    },
+    connectionContainer: {
+      width: 500,
+      margin: theme.spacing(4)
+    }
+  };
+});
+
+function ToggleConnectionDialog(_ref) {
+  var session = _ref.session,
+      handleClose = _ref.handleClose,
+      assemblyName = _ref.assemblyName,
+      breakConnection = _ref.breakConnection;
+  var classes = useStyles();
+  var connections = session.connections,
+      connectionInstances = session.connectionInstances;
+  var assemblySpecificConnections = connections.filter(function (c) {
+    var configAssemblyNames = (0, _configuration.readConfObject)(c, 'assemblyNames');
+
+    if (configAssemblyNames.length === 0) {
+      return true;
+    }
+
+    return configAssemblyNames.includes(assemblyName);
+  });
+  return /*#__PURE__*/_react["default"].createElement(_core.Dialog, {
+    open: true,
+    onClose: handleClose,
+    maxWidth: "lg"
+  }, /*#__PURE__*/_react["default"].createElement(_core.DialogTitle, null, "Turn on/off connections", /*#__PURE__*/_react["default"].createElement(_core.IconButton, {
+    className: classes.closeButton,
+    onClick: function onClick() {
+      return handleClose();
+    }
+  }, /*#__PURE__*/_react["default"].createElement(_Close["default"], null))), /*#__PURE__*/_react["default"].createElement(_core.DialogContent, null, /*#__PURE__*/_react["default"].createElement(_core.Typography, null, "Use the checkbox to turn on/off connections"), /*#__PURE__*/_react["default"].createElement("div", {
+    className: classes.connectionContainer
+  }, assemblySpecificConnections.map(function (conf) {
+    var name = (0, _configuration.readConfObject)(conf, 'name');
+    return /*#__PURE__*/_react["default"].createElement("div", {
+      key: conf.connectionId
+    }, /*#__PURE__*/_react["default"].createElement(_core.FormControlLabel, {
+      control: /*#__PURE__*/_react["default"].createElement(_core.Checkbox, {
+        checked: !!(connectionInstances !== null && connectionInstances !== void 0 && connectionInstances.find(function (conn) {
+          return name === conn.name;
+        })),
+        onChange: function onChange() {
+          if (connectionInstances !== null && connectionInstances !== void 0 && connectionInstances.find(function (conn) {
+            return conn.name === (0, _configuration.readConfObject)(conf, 'name');
+          })) {
+            breakConnection(conf);
+          } else {
+            var _session$makeConnecti;
+
+            (_session$makeConnecti = session.makeConnection) === null || _session$makeConnecti === void 0 ? void 0 : _session$makeConnecti.call(session, conf);
+          }
+        },
+        color: "primary"
+      }),
+      label: name
+    }));
+  }), !assemblySpecificConnections.length ? /*#__PURE__*/_react["default"].createElement(_core.Typography, null, "No connections found for ", assemblyName) : null)), /*#__PURE__*/_react["default"].createElement(_core.DialogActions, null, /*#__PURE__*/_react["default"].createElement(_core.Button, {
+    onClick: function onClick() {
+      return handleClose();
+    },
+    variant: "contained",
+    color: "primary"
+  }, "Close")));
+}
+
+var _default = (0, _mobxReact.observer)(ToggleConnectionDialog);
+
+exports["default"] = _default;

package/dist/HierarchicalTrackSelectorWidget/index.js

@@ -0,0 +1,21 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.configSchema = void 0;
+Object.defineProperty(exports, "stateModelFactory", {
+  enumerable: true,
+  get: function get() {
+    return _model["default"];
+  }
+});
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _model = _interopRequireDefault(require("./model"));
+
+var configSchema = (0, _configuration.ConfigurationSchema)('HierarchicalTrackSelectorWidget', {});
+exports.configSchema = configSchema;