@jbrowse/plugin-data-management 1.7.11 → 2.0.0

package/dist/AddTrackWidget/index.test.js

@@ -1,292 +0,0 @@
-"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 () {
-    console.warn = jest.fn();
-    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');
-  });
-});

package/dist/AssemblyManager/AssemblyManager.test.js

@@ -1,113 +0,0 @@
-"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/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.test.js

@@ -1,191 +0,0 @@
-"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/model.test.js

@@ -1,28 +0,0 @@
-"use strict";
-
-var _model = require("./model");
-
-xtest('can generate hierarchy correctly', function () {
-  var trackConfigurations = [{
-    trackId: 'zonker',
-    category: {
-      expr: {
-        evalSync: function evalSync() {
-          return ['Bar', 'Baz'];
-        }
-      }
-    }
-  }, {
-    trackId: 'zoo'
-  }, {
-    trackId: 'bee',
-    category: {
-      expr: {
-        evalSync: function evalSync() {
-          return ['Bar'];
-        }
-      }
-    }
-  }];
-  expect((0, _model.generateHierarchy)(trackConfigurations)).toEqual(new Map([['Bar', new Map([['bee', trackConfigurations[2]], ['Baz', new Map([['zonker', trackConfigurations[0]]])]])], ['zoo', trackConfigurations[1]]]));
-});