@jbrowse/plugin-data-management 1.6.7 → 1.7.0

package/dist/AddTrackWidget/components/ConfirmTrack.js

@@ -0,0 +1,277 @@
+"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 _configuration = require("@jbrowse/core/configuration");
+
+var _util = require("@jbrowse/core/util");
+
+var _core = require("@material-ui/core");
+
+var _mobxReact = require("mobx-react");
+
+var _mobxStateTree = require("mobx-state-tree");
+
+var _tracks = require("@jbrowse/core/util/tracks");
+
+var useStyles = (0, _core.makeStyles)(function (theme) {
+  return {
+    spacing: {
+      marginBottom: theme.spacing(3)
+    }
+  };
+});
+
+function StatusMessage(_ref) {
+  var _trackAdapter$subadap;
+
+  var trackAdapter = _ref.trackAdapter,
+      trackType = _ref.trackType;
+  var classes = useStyles();
+  return trackAdapter.type === 'SNPCoverageAdapter' ? /*#__PURE__*/_react["default"].createElement(_core.Typography, {
+    className: classes.spacing
+  }, "Selected ", /*#__PURE__*/_react["default"].createElement("code", null, trackType), ". Using adapter", ' ', /*#__PURE__*/_react["default"].createElement("code", null, trackAdapter.type), " with subadapter", ' ', /*#__PURE__*/_react["default"].createElement("code", null, (_trackAdapter$subadap = trackAdapter.subadapter) === null || _trackAdapter$subadap === void 0 ? void 0 : _trackAdapter$subadap.type), ". Please enter a track name and, if necessary, update the track type.") : /*#__PURE__*/_react["default"].createElement(_core.Typography, {
+    className: classes.spacing
+  }, "Using adapter ", /*#__PURE__*/_react["default"].createElement("code", null, trackAdapter.type), " and guessing track type", ' ', /*#__PURE__*/_react["default"].createElement("code", null, trackType), ". Please enter a track name and, if necessary, update the track type.");
+}
+/**
+ * categorizeAdapters takes a list of adapters and sorts their menu item elements under an appropriate ListSubheader
+ *  element. In this way, adapters that are from external plugins can have headers that differentiate them from the
+ *  out-of-the-box plugins.
+ * @param adaptersList - a list of adapters found in the PluginManager
+ * @returns a series of JSX elements that are ListSubheaders followed by the adapters
+ *   found under that subheader
+ */
+
+
+function categorizeAdapters(adaptersList) {
+  var currentCategory = ''; // eslint-disable-next-line @typescript-eslint/no-explicit-any
+
+  var items = [];
+  adaptersList.forEach(function (adapter) {
+    var _adapter$adapterMetad;
+
+    if ((_adapter$adapterMetad = adapter.adapterMetadata) !== null && _adapter$adapterMetad !== void 0 && _adapter$adapterMetad.category) {
+      var _adapter$adapterMetad2, _adapter$adapterMetad7, _adapter$adapterMetad8;
+
+      if (currentCategory !== ((_adapter$adapterMetad2 = adapter.adapterMetadata) === null || _adapter$adapterMetad2 === void 0 ? void 0 : _adapter$adapterMetad2.category)) {
+        var _adapter$adapterMetad3, _adapter$adapterMetad4, _adapter$adapterMetad5, _adapter$adapterMetad6;
+
+        currentCategory = (_adapter$adapterMetad3 = adapter.adapterMetadata) === null || _adapter$adapterMetad3 === void 0 ? void 0 : _adapter$adapterMetad3.category;
+        items.push( /*#__PURE__*/_react["default"].createElement(_core.ListSubheader, {
+          key: (_adapter$adapterMetad4 = adapter.adapterMetadata) === null || _adapter$adapterMetad4 === void 0 ? void 0 : _adapter$adapterMetad4.category,
+          value: (_adapter$adapterMetad5 = adapter.adapterMetadata) === null || _adapter$adapterMetad5 === void 0 ? void 0 : _adapter$adapterMetad5.category
+        }, (_adapter$adapterMetad6 = adapter.adapterMetadata) === null || _adapter$adapterMetad6 === void 0 ? void 0 : _adapter$adapterMetad6.category));
+      }
+
+      items.push( /*#__PURE__*/_react["default"].createElement(_core.MenuItem, {
+        key: adapter.name,
+        value: adapter.name
+      }, (_adapter$adapterMetad7 = adapter.adapterMetadata) !== null && _adapter$adapterMetad7 !== void 0 && _adapter$adapterMetad7.displayName ? (_adapter$adapterMetad8 = adapter.adapterMetadata) === null || _adapter$adapterMetad8 === void 0 ? void 0 : _adapter$adapterMetad8.displayName : adapter.name));
+    }
+  });
+  return items;
+}
+
+function getAdapterTypes(pluginManager) {
+  return pluginManager.getElementTypesInGroup('adapter');
+}
+
+function getTrackTypes(pluginManager) {
+  return pluginManager.getElementTypesInGroup('track');
+}
+
+var TrackAdapterSelector = (0, _mobxReact.observer)(function (_ref2) {
+  var model = _ref2.model;
+  var classes = useStyles();
+  var session = (0, _util.getSession)(model);
+  var trackAdapter = model.trackAdapter; // prettier-ignore
+
+  var adapters = getAdapterTypes((0, _mobxStateTree.getEnv)(session).pluginManager);
+  return /*#__PURE__*/_react["default"].createElement(_core.TextField, {
+    className: classes.spacing,
+    value: (trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type) !== 'UNKNOWN' ? trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type : '',
+    label: "adapterType",
+    helperText: "Select an adapter type",
+    select: true,
+    fullWidth: true,
+    onChange: function onChange(event) {
+      model.setAdapterHint(event.target.value);
+    },
+    SelectProps: {
+      // @ts-ignore
+      SelectDisplayProps: {
+        'data-testid': 'adapterTypeSelect'
+      }
+    }
+  }, adapters // Excludes any adapter with the 'adapterMetadata.hiddenFromGUI' property, and anything with the 'adapterMetadata.category' property
+  .filter(function (elt) {
+    var _elt$adapterMetadata, _elt$adapterMetadata2;
+
+    return !((_elt$adapterMetadata = elt.adapterMetadata) !== null && _elt$adapterMetadata !== void 0 && _elt$adapterMetadata.hiddenFromGUI) && !((_elt$adapterMetadata2 = elt.adapterMetadata) !== null && _elt$adapterMetadata2 !== void 0 && _elt$adapterMetadata2.category);
+  }).map(function (elt) {
+    var _elt$adapterMetadata3, _elt$adapterMetadata4;
+
+    return /*#__PURE__*/_react["default"].createElement(_core.MenuItem, {
+      key: elt.name,
+      value: elt.name
+    }, (_elt$adapterMetadata3 = elt.adapterMetadata) !== null && _elt$adapterMetadata3 !== void 0 && _elt$adapterMetadata3.displayName ? (_elt$adapterMetadata4 = elt.adapterMetadata) === null || _elt$adapterMetadata4 === void 0 ? void 0 : _elt$adapterMetadata4.displayName : elt.name);
+  }), categorizeAdapters(adapters.filter(function (elt) {
+    var _elt$adapterMetadata5;
+
+    return !((_elt$adapterMetadata5 = elt.adapterMetadata) !== null && _elt$adapterMetadata5 !== void 0 && _elt$adapterMetadata5.hiddenFromGUI);
+  })));
+});
+
+function UnknownAdapterPrompt(_ref3) {
+  var model = _ref3.model;
+  var classes = useStyles();
+  return /*#__PURE__*/_react["default"].createElement(_react["default"].Fragment, null, /*#__PURE__*/_react["default"].createElement(_core.Typography, {
+    className: classes.spacing
+  }, "JBrowse was not able to guess the adapter type for this data, but it may be in the list below. If not, you can", ' ', /*#__PURE__*/_react["default"].createElement(_core.Link, {
+    href: "https://github.com/GMOD/jbrowse-components/releases",
+    target: "_blank",
+    rel: "noopener noreferrer"
+  }, "check for new releases"), ' ', "of JBrowse to see if they support this data type or", ' ', /*#__PURE__*/_react["default"].createElement(_core.Link, {
+    href: "https://github.com/GMOD/jbrowse-components/issues/new",
+    target: "_blank",
+    rel: "noopener noreferrer"
+  }, "file an issue"), ' ', "and add a feature request for this data type."), /*#__PURE__*/_react["default"].createElement(TrackAdapterSelector, {
+    model: model
+  }));
+}
+
+var TrackTypeSelector = (0, _mobxReact.observer)(function (_ref4) {
+  var model = _ref4.model;
+  var classes = useStyles();
+  var session = (0, _util.getSession)(model);
+  var trackType = model.trackType;
+  var trackTypes = getTrackTypes((0, _mobxStateTree.getEnv)(session).pluginManager);
+  return /*#__PURE__*/_react["default"].createElement(_core.TextField, {
+    className: classes.spacing,
+    value: trackType,
+    label: "trackType",
+    helperText: "Select a track type",
+    select: true,
+    fullWidth: true,
+    onChange: function onChange(event) {
+      model.setTrackType(event.target.value);
+    },
+    SelectProps: {
+      // @ts-ignore
+      SelectDisplayProps: {
+        'data-testid': 'trackTypeSelect'
+      }
+    }
+  }, trackTypes.map(function (_ref5) {
+    var name = _ref5.name;
+    return /*#__PURE__*/_react["default"].createElement(_core.MenuItem, {
+      key: name,
+      value: name
+    }, name);
+  }));
+});
+var TrackAssemblySelector = (0, _mobxReact.observer)(function (_ref6) {
+  var model = _ref6.model;
+  var session = (0, _util.getSession)(model);
+  var assembly = model.assembly;
+  return /*#__PURE__*/_react["default"].createElement(_core.TextField, {
+    value: assembly,
+    label: "assemblyName",
+    helperText: "Assembly to which the track will be added",
+    select: true,
+    fullWidth: true,
+    onChange: function onChange(event) {
+      return model.setAssembly(event.target.value);
+    },
+    SelectProps: {
+      // @ts-ignore
+      SelectDisplayProps: {
+        'data-testid': 'assemblyNameSelect'
+      }
+    }
+  }, session.assemblies.map(function (conf) {
+    return (0, _configuration.readConfObject)(conf, 'name');
+  }).map(function (name) {
+    return /*#__PURE__*/_react["default"].createElement(_core.MenuItem, {
+      key: name,
+      value: name
+    }, name);
+  }));
+});
+
+function ConfirmTrack(_ref7) {
+  var model = _ref7.model;
+  var classes = useStyles();
+  var trackName = model.trackName,
+      trackAdapter = model.trackAdapter,
+      trackType = model.trackType,
+      warningMessage = model.warningMessage,
+      adapterHint = model.adapterHint;
+
+  if (model.unsupported) {
+    return /*#__PURE__*/_react["default"].createElement(_core.Typography, {
+      className: classes.spacing
+    }, "This version of JBrowse cannot display data of this type. It is possible, however, that there is a newer version that can display them. You can", ' ', /*#__PURE__*/_react["default"].createElement(_core.Link, {
+      href: "https://github.com/GMOD/jbrowse-components/releases",
+      target: "_blank",
+      rel: "noopener noreferrer"
+    }, "check for new releases"), ' ', "of JBrowse or", ' ', /*#__PURE__*/_react["default"].createElement(_core.Link, {
+      href: "https://github.com/GMOD/jbrowse-components/issues/new",
+      target: "_blank",
+      rel: "noopener noreferrer"
+    }, "file an issue"), ' ', "and add a feature request for this data type.");
+  }
+
+  if ((trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type) === _tracks.UNKNOWN) {
+    return /*#__PURE__*/_react["default"].createElement(UnknownAdapterPrompt, {
+      model: model
+    });
+  }
+
+  if (adapterHint === '' && trackAdapter) {
+    model.setAdapterHint(trackAdapter.type);
+  }
+
+  if (!(trackAdapter !== null && trackAdapter !== void 0 && trackAdapter.type)) {
+    return /*#__PURE__*/_react["default"].createElement(_core.Typography, null, "Could not recognize this data type.");
+  }
+
+  return /*#__PURE__*/_react["default"].createElement("div", null, trackAdapter ? /*#__PURE__*/_react["default"].createElement(StatusMessage, {
+    trackAdapter: trackAdapter,
+    trackType: trackType
+  }) : null, warningMessage ? /*#__PURE__*/_react["default"].createElement(_core.Typography, {
+    style: {
+      color: 'orange'
+    }
+  }, warningMessage) : null, /*#__PURE__*/_react["default"].createElement(_core.TextField, {
+    className: classes.spacing,
+    label: "trackName",
+    helperText: "A name for this track",
+    fullWidth: true,
+    value: trackName,
+    onChange: function onChange(event) {
+      return model.setTrackName(event.target.value);
+    },
+    inputProps: {
+      'data-testid': 'trackNameInput'
+    }
+  }), /*#__PURE__*/_react["default"].createElement(TrackAdapterSelector, {
+    model: model
+  }), /*#__PURE__*/_react["default"].createElement(TrackTypeSelector, {
+    model: model
+  }), /*#__PURE__*/_react["default"].createElement(TrackAssemblySelector, {
+    model: model
+  }));
+}
+
+var _default = (0, _mobxReact.observer)(ConfirmTrack);
+
+exports["default"] = _default;

package/dist/AddTrackWidget/components/TrackSourceSelect.js

@@ -0,0 +1,60 @@
+"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 _ui = require("@jbrowse/core/ui");
+
+var _core = require("@material-ui/core");
+
+var _mobxStateTree = require("mobx-state-tree");
+
+var _mobxReact = require("mobx-react");
+
+var useStyles = (0, _core.makeStyles)(function (theme) {
+  return {
+    paper: {
+      display: 'flex',
+      flexDirection: 'column',
+      padding: theme.spacing(1)
+    },
+    spacer: {
+      height: theme.spacing(8)
+    }
+  };
+});
+
+function TrackSourceSelect(_ref) {
+  var model = _ref.model;
+  var classes = useStyles();
+  var rootModel = (0, _mobxStateTree.getRoot)(model);
+  return /*#__PURE__*/_react["default"].createElement(_core.Paper, {
+    className: classes.paper
+  }, /*#__PURE__*/_react["default"].createElement(_ui.FileSelector, {
+    name: "Main file",
+    description: "",
+    location: model.trackData,
+    setLocation: model.setTrackData,
+    setName: model.setTrackName,
+    rootModel: rootModel
+  }), /*#__PURE__*/_react["default"].createElement("div", {
+    className: classes.spacer
+  }), /*#__PURE__*/_react["default"].createElement(_ui.FileSelector, {
+    name: "Index file",
+    description: "(Optional) The URL of the index file is automatically inferred from the URL of the main file if it is not supplied.",
+    location: model.indexTrackData,
+    setLocation: model.setIndexTrackData,
+    setName: model.setTrackName,
+    rootModel: rootModel
+  }));
+}
+
+var _default = (0, _mobxReact.observer)(TrackSourceSelect);
+
+exports["default"] = _default;

package/dist/AddTrackWidget/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)('AddTrackWidget', {});
+exports.configSchema = configSchema;

package/dist/AddTrackWidget/index.test.js

@@ -0,0 +1,291 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+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 = _interopRequireDefault(require("react"));
+
+var _mobxStateTree = require("mobx-state-tree");
+
+var _PluginManager = _interopRequireDefault(require("@jbrowse/core/PluginManager"));
+
+var _Plugin2 = _interopRequireDefault(require("@jbrowse/core/Plugin"));
+
+var _ViewType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/ViewType"));
+
+var _model = _interopRequireDefault(require("./model"));
+
+var _pluginAlignments = _interopRequireDefault(require("@jbrowse/plugin-alignments"));
+
+var _pluginSvg = _interopRequireDefault(require("@jbrowse/plugin-svg"));
+
+var _pluginVariants = _interopRequireDefault(require("@jbrowse/plugin-variants"));
+
+var _pluginHic = _interopRequireDefault(require("@jbrowse/plugin-hic"));
+
+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; } }
+
+function standardInitializer() {
+  var pluginManager = new _PluginManager["default"]([new FakeViewPlugin(), new _pluginAlignments["default"](), new _pluginSvg["default"](), new _pluginVariants["default"](), new _pluginHic["default"]()]);
+  pluginManager.createPluggableElements();
+  pluginManager.configure();
+
+  var SessionModel = _mobxStateTree.types.model({
+    view: FakeViewModel,
+    widget: (0, _model["default"])(pluginManager)
+  })["volatile"](function () {
+    return {
+      rpcManager: {},
+      configuration: {}
+    };
+  }); // assemblyNames is defined on the view, which is done in LGV for example
+  // this is really just used for convenience to automatically fill in the
+  // assembly field in the form
+
+
+  return SessionModel.create({
+    view: {
+      id: 'testing',
+      type: 'FakeView',
+      assemblyNames: ['volvox']
+    },
+    widget: {
+      type: 'AddTrackWidget',
+      view: 'testing'
+    }
+  }, {
+    pluginManager: pluginManager
+  });
+}
+
+var realLocation = window.location; // https://stackoverflow.com/a/60110508/2129219
+
+function setWindowLoc(loc) {
+  delete window.location;
+  window.location = new URL(loc);
+}
+
+var FakeViewModel = _mobxStateTree.types.model('FakeView', {
+  id: _mobxStateTree.types.identifier,
+  type: _mobxStateTree.types.literal('FakeView'),
+  assemblyNames: _mobxStateTree.types.maybe(_mobxStateTree.types.array(_mobxStateTree.types.string))
+}); // register a true fake view plugin because the widget.view is a true
+// safeReference to a pluginManager.pluggableMstType('view', 'stateModel')
+
+
+var FakeViewPlugin = /*#__PURE__*/function (_Plugin) {
+  (0, _inherits2["default"])(FakeViewPlugin, _Plugin);
+
+  var _super = _createSuper(FakeViewPlugin);
+
+  function FakeViewPlugin() {
+    var _this;
+
+    (0, _classCallCheck2["default"])(this, FakeViewPlugin);
+
+    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", 'FakeViewPlugin');
+    return _this;
+  }
+
+  (0, _createClass2["default"])(FakeViewPlugin, [{
+    key: "install",
+    value: function install(pluginManager) {
+      pluginManager.addViewType(function () {
+        return new _ViewType["default"]({
+          name: 'FakeView',
+          stateModel: FakeViewModel,
+          ReactComponent: function ReactComponent() {
+            return /*#__PURE__*/_react["default"].createElement("div", null, "Hello world");
+          }
+        });
+      });
+    }
+  }]);
+  return FakeViewPlugin;
+}(_Plugin2["default"]);
+
+describe('tests on an LGV type system with view.assemblyNames, using URL', function () {
+  var session;
+  beforeEach(function () {
+    session = standardInitializer();
+  });
+  afterEach(function () {
+    window.location = realLocation;
+  });
+  it('adds relative URL (BAM)', function () {
+    var _session = session,
+        widget = _session.widget;
+    widget.setTrackData({
+      uri: 'volvox-sorted.bam',
+      locationType: 'UriLocation'
+    });
+    expect(widget.trackName).toBe('volvox-sorted.bam');
+    expect(widget.isFtp).toBe(false);
+    expect(widget.isRelativeUrl).toBe(true);
+    expect(widget.assembly).toBe('volvox');
+    expect(widget.trackType).toBe('AlignmentsTrack');
+  });
+  it('adds full URL (BAM)', function () {
+    var _session2 = session,
+        widget = _session2.widget;
+    widget.setTrackData({
+      uri: 'http://google.com/volvox-sorted.bam',
+      locationType: 'UriLocation'
+    });
+    expect(widget.trackName).toBe('volvox-sorted.bam');
+    expect(widget.isRelativeUrl).toBe(false);
+    expect(widget.assembly).toBe('volvox');
+  });
+  it('test wrongProtocol returning false', function () {
+    var _session3 = session,
+        widget = _session3.widget;
+    widget.setTrackData({
+      uri: 'http://google.com/volvox-sorted.bam',
+      locationType: 'UriLocation'
+    });
+    setWindowLoc('http://google.com');
+    expect(widget.wrongProtocol).toBe(false);
+  });
+  it('test wrongProtocol returning true', function () {
+    var _session4 = session,
+        widget = _session4.widget;
+    widget.setTrackData({
+      uri: 'http://google.com/volvox-sorted.bam',
+      locationType: 'UriLocation'
+    });
+    setWindowLoc('https://google.com');
+    expect(widget.wrongProtocol).toBe(true);
+  });
+});
+describe('tests on an view without view.assemblyNames', function () {
+  var session;
+  beforeEach(function () {
+    var pluginManager = new _PluginManager["default"]([new FakeViewPlugin()]);
+    pluginManager.createPluggableElements();
+    pluginManager.configure();
+
+    var SessionModel = _mobxStateTree.types.model({
+      view: FakeViewModel,
+      widget: (0, _model["default"])(pluginManager)
+    }); // no assemblyNames on the view, just in case some view does not implement
+    // view.assemblyNames (it is just a convenience)
+
+
+    session = SessionModel.create({
+      view: {
+        type: 'FakeView',
+        id: 'testing'
+      },
+      widget: {
+        type: 'AddTrackWidget',
+        view: 'testing'
+      }
+    });
+  });
+  it('adds url', function () {
+    var _session5 = session,
+        widget = _session5.widget;
+    widget.setTrackData({
+      uri: 'volvox-sorted.bam',
+      locationType: 'UriLocation'
+    });
+    expect(widget.trackName).toBe('volvox-sorted.bam');
+    expect(widget.isRelativeUrl).toBe(true);
+    expect(widget.assembly).toBe(undefined);
+  });
+});
+describe('tests different file types', function () {
+  var session;
+  beforeEach(function () {
+    session = standardInitializer();
+  });
+  afterEach(function () {
+    window.location = realLocation;
+  });
+  it('adds bam', function () {
+    var _session6 = session,
+        widget = _session6.widget;
+    widget.setTrackData({
+      uri: 'volvox-sorted.bam',
+      locationType: 'UriLocation'
+    });
+    expect(widget.trackType).toBe('AlignmentsTrack');
+  });
+  it('adds cram', function () {
+    var _session7 = session,
+        widget = _session7.widget;
+    widget.setTrackData({
+      uri: 'volvox-sorted.cram',
+      locationType: 'UriLocation'
+    });
+    expect(widget.trackType).toBe('AlignmentsTrack');
+  });
+  it('adds .vcf.gz', function () {
+    var _session8 = session,
+        widget = _session8.widget;
+    widget.setTrackData({
+      uri: 'volvox-sorted.vcf.gz',
+      locationType: 'UriLocation'
+    });
+    expect(widget.trackType).toBe('VariantTrack');
+  });
+  it('adds .gff3', function () {
+    var _session9 = session,
+        widget = _session9.widget;
+    widget.setTrackData({
+      uri: 'volvox-sorted.gff3',
+      locationType: 'UriLocation'
+    });
+    expect(widget.trackType).toBe('FeatureTrack');
+  });
+  it('adds .hic', function () {
+    var _session10 = session,
+        widget = _session10.widget;
+    widget.setTrackData({
+      uri: 'volvox-sorted.hic',
+      locationType: 'UriLocation'
+    });
+    expect(widget.trackType).toBe('HicTrack');
+  });
+});
+describe('tests localpath', function () {
+  var session;
+  beforeEach(function () {
+    session = standardInitializer();
+  });
+  it('adds bam', function () {
+    var _session11 = session,
+        widget = _session11.widget;
+    widget.setTrackData({
+      localPath: 'volvox-sorted.bam',
+      locationType: 'LocalPathLocation'
+    });
+    expect(widget.trackType).toBe('AlignmentsTrack');
+    expect(widget.trackName).toBe('volvox-sorted.bam'); // the localPath is not a "relativeUrl"
+
+    expect(widget.isRelativeUrl).toBe(false);
+    expect(widget.isFtp).toBe(false);
+    expect(widget.wrongProtocol).toBe(false);
+    expect(widget.assembly).toBe('volvox');
+  });
+});